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+++ b/archive/citation_metadata_academic_impact/PHANOTATE.json
@@ -1,9 +1,9 @@
 {
-  "name": "PHANOTATE",
+  "name": "Phanotate",
   "url": "https://github.com/deprekate/PHANOTATE",
   "doi": null,
   "citation_info": {},
   "citation_metrics": {},
   "related_papers": [],
-  "last_updated": "2025-11-01T12:45:25.280466"
+  "last_updated": "2025-11-01T12:46:07.361315"
 }
\ No newline at end of file

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	modified:   archive/citation_metadata_academic_impact/Phanotate.json
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	modified:   archive/citation_metadata_academic_impact/PHANOTATE.json
	modified:   archive/citation_metadata_academic_impact/PhageBoost.json
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-rw-r--r--@   1 scotthandley  staff      216 Nov 29 15:28 PHANOTATE-AMR.json
-rw-r--r--@   1 scotthandley  staff      212 Nov 29 15:57 Phanotate.json

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	modified:   archive/citation_metadata_academic_impact/Phanotate.json
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6 files changed, 15 insertions(+), 15 deletions(-)
To https://github.com/shandley/awesome-virome.git
   9ccbbbf69..8ac6ff594  main -> main

Todos have been modified successfully. Ensure that you continue to use the todo list to track your progress. Please proceed with the current tasks if applicable

     1→<img src="awesome-virome-hex.png" align="left" width="180" style="margin-right: 25px; margin-bottom: 20px;" />
     2→
     3→# Awesome-Virome
     4→
     5→[![Awesome](https://awesome.re/badge.svg)](https://awesome.re)
     6→[![Data Update Status](https://github.com/shandley/awesome-virome/actions/workflows/simplified-update-workflow.yml/badge.svg)](https://github.com/shandley/awesome-virome/actions/workflows/simplified-update-workflow.yml)
     7→[![Site Health](https://github.com/shandley/awesome-virome/actions/workflows/site-health-check.yml/badge.svg)](https://github.com/shandley/awesome-virome/actions/workflows/site-health-check.yml)
     8→[![Cache Status](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/shandley/awesome-virome/main/.github/badges/cache-status.json)](https://github.com/shandley/awesome-virome/actions/workflows/cache-maintenance.yml)
     9→
    10→<br clear="left"/>
    11→
    12→## What is Awesome-Virome?
    13→
    14→A comprehensive, curated database of **300+ software tools** for virome analysis - the study of viral communities in various environments. This repository helps researchers navigate the complex landscape of tools for analyzing phages, viruses, and their interactions with hosts.
    15→
    16→**🎯 Perfect for:**
    17→- Researchers new to virome analysis seeking guidance
    18→- Experienced scientists looking for specific tools
    19→- Developers building viral analysis workflows
    20→- Students learning computational virology
    21→
    22→**🚀 Key Features:**
    23→- Curated collection of 300+ tools across 8 major categories
    24→- Interactive dashboard with visualization and analytics
    25→- Tool comparison matrix with filtering and export
    26→- Automated metadata collection from GitHub/GitLab/Bitbucket
    27→- RESTful API for programmatic access
    28→- Weekly updates and quality assurance
    29→
    30→## Quick Start Guide
    31→
    32→**New to virome analysis?** Here are the essential tools to get you started:
    33→
    34→| Analysis Step | Recommended Tools | Purpose |
    35→|---------------|-------------------|---------|
    36→| **1. Viral identification** | VirSorter2, VIBRANT, geNomad | Find viral sequences in metagenomic data |
    37→| **2. Quality control** | CheckV | Assess viral genome completeness and quality |
    38→| **3. Host prediction** | iPHoP, CHERRY | Predict which hosts viruses infect |
    39→| **4. Genome annotation** | Pharokka, DRAMv | Annotate viral genes and functions |
    40→| **5. Taxonomy assignment** | vConTACT2, PhaGCN | Classify viruses taxonomically |
    41→
    42→**Basic Virome Analysis Workflow:**
    43→1. Quality control of metagenomic reads
    44→2. Assembly of contigs (e.g., SPAdes, MEGAHIT)
    45→3. Identification of viral contigs → [Virus and Phage Identification](#virus-and-phage-identification)
    46→4. Quality assessment → [Genome Analysis](#genome-analysis)
    47→5. Taxonomic classification → [Taxonomy](#taxonomy)
    48→6. Host prediction → [Host Prediction](#host-prediction)
    49→7. Functional annotation → [Functional Analysis](#functional-analysis)
    50→
    51→**🎯 Quick Access:**
    52→- [**Browse All Tools by Category**](#virus-and-phage-identification) ↓
    53→- [**Interactive Dashboard**](https://shandley.github.io/awesome-virome/dashboard.html) - Visualize tool relationships
    54→- [**Tool Comparison Matrix**](https://shandley.github.io/awesome-virome/comparison.html) - Compare tools side-by-side
    55→- [**Selection Guide**](https://shandley.github.io/awesome-virome/selection-guide.html) - Get personalized recommendations
    56→
    57→## Top Tools by Category
    58→
    59→Here are the most popular and well-maintained tools in each major category:
    60→
    61→### 🦠 Virus and Phage Identification
    62→| Tool | Stars | Description |
    63→|------|-------|-------------|
    64→| [BLAST+DIAMOND](https://github.com/bbuchfink/diamond) | ⭐ 1114 | Fast sequence similarity search |
    65→| [geNomad](https://github.com/apcamargo/genomad) [v1.6.0, 2023] | ⭐ 219 | ML-based virus identification including proviruses |
    66→| [VIBRANT](https://github.com/AnantharamanLab/VIBRANT) | ⭐ 159 | Virus identification by boundary detection + annotation |
    67→
    68→### 🎯 Host Prediction
    69→| Tool | Stars | Description |
    70→|------|-------|-------------|
    71→| [CHERRY](https://github.com/KennthShang/CHERRY) [v1.0, 2022] | ⭐ 24 | Deep learning for phage host prediction |
    72→| [VirHostMatcher-Net](https://github.com/WeiliWw/VirHostMatcher-Net) | ⭐ 21 | Network-based virus-host prediction |
    73→| [DeepHost](https://github.com/deepomicslab/DeepHost) | ⭐ 17 | CNN for phage host prediction |
    74→
    75→### 🧬 Genome Analysis
    76→| Tool | Stars | Description |
    77→|------|-------|-------------|
    78→| [metaviralSPAdes](https://github.com/ablab/spades/tree/metaviral_publication) | ⭐ 797 | Assembler for viruses from metagenomic data |
    79→| [Prodigal/MetaProdigal](https://github.com/hyattpd/Prodigal) | ⭐ 471 | Gene prediction for prokaryotic genomes |
    80→| [Pharokka](https://github.com/gbouras13/pharokka) [v1.5.0, 2023] | ⭐ 158 | Rapid phage annotation tool |
    81→
    82→### 📊 Taxonomy
    83→| Tool | Stars | Description |
    84→|------|-------|-------------|
    85→| [vConTACT2.0](https://bitbucket.org/MAVERICLab/vcontact2/src/master/) [v0.9.19, 2023] | ⭐ 27 | Genome-sharing networks for virus taxonomy |
    86→| [PhaGCN](https://github.com/KennthShang/PhaGCN) [v1.0, 2022] | ⭐ 25 | Graph convolutional network for phage taxonomy |
    87→| [VIPtree](https://github.com/yosuken/ViPTreeGen) | ⭐ 19 | Viral proteomic tree generation |
    88→
    89→**📈 Most Starred Overall:**
    90→1. [AlphaFold-Multimer](https://github.com/deepmind/alphafold) (⭐ 13320) - Protein structure prediction
    91→2. [CovidMD](https://github.com/lammps/lammps) (⭐ 2365) - Molecular dynamics for COVID-19
    92→3. [BLAST+DIAMOND](https://github.com/bbuchfink/diamond) (⭐ 1114) - Fast sequence alignment
    93→
    94→## Contents
    95→
    96→### 🚀 Getting Started
    97→- [What is Awesome-Virome?](#what-is-awesome-virome)
    98→- [Quick Start Guide](#quick-start-guide)
    99→- [Top Tools by Category](#top-tools-by-category)
   100→

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

   100→
   101→### 🔧 Core Analysis Tools
   102→- [Virus and Phage Identification](#virus-and-phage-identification)
   103→  - [Metagenome Analysis](#metagenome-analysis)
   104→  - [Integrated Viruses](#integrated-viruses)
   105→  - [RNA Virus Identification](#rna-virus-identification)
   106→- [Host Prediction](#host-prediction)
   107→- [Genome Analysis](#genome-analysis)
   108→  - [Genome Annotation](#genome-annotation)
   109→  - [Genome Assembly](#genome-assembly)
   110→  - [Genome Completeness](#genome-completeness)
   111→  - [Genome Comparison](#genome-comparison)
   112→  - [Gene Finding](#gene-finding)
   113→- [Taxonomy](#taxonomy)
   114→
   115→### 📊 Data Resources
   116→- [Databases](#databases)
   117→- [Sequence Databases](#sequence-databases)
   118→
   119→### 🧪 Specialized Analysis
   120→- [Functional Analysis](#functional-analysis)
   121→  - [Evolutionary Analysis](#evolutionary-analysis)
   122→  - [Lifestyle Classification](#lifestyle-classification)
   123→  - [Phage-specific Analysis](#phage-specific-analysis)
   124→  - [Viral Orthologous Groups](#viral-orthologous-groups)
   125→- [Sequence Analysis](#sequence-analysis)
   126→- [CRISPR Analysis](#crispr-analysis)
   127→- [Other Tools](#other-tools)
   128→
   129→### 🌐 Interactive Features
   130→- [Interactive Dashboard](#interactive-dashboard)
   131→- [Tool Comparison Matrix](#tool-comparison-matrix)
   132→- [Tool Selection Guide](#tool-selection-guide)
   133→- [API Support](#api-support)
   134→
   135→### 📚 Project Information
   136→- [Introduction to Virome Analysis](#introduction-to-virome-analysis)
   137→- [Contributing](#contributing)
   138→- [Repository Maintenance](#repository-maintenance)
   139→- [Acknowledgments](#acknowledgments)
   140→- [License](#license)
   141→
   142→---
   143→
   144→## Typical Workflows
   145→
   146→### Basic Virome Analysis Workflow:
   147→1. Quality control of metagenomic reads
   148→2. Assembly of contigs (e.g., SPAdes, MEGAHIT)
   149→3. Identification of viral contigs → [Virus and Phage Identification](#virus-and-phage-identification)
   150→4. Quality assessment → [Genome Analysis](#genome-analysis)
   151→5. Taxonomic classification → [Taxonomy](#taxonomy)
   152→6. Host prediction → [Host Prediction](#host-prediction)
   153→7. Functional annotation → [Functional Analysis](#functional-analysis)
   154→
   155→### Advanced Analysis Options:
   156→- **Strain reconstruction**: [Viral Strain Reconstruction](#viral-strain-reconstruction)
   157→- **Host-virus interactions**: [Interaction Analysis](#interaction-analysis)
   158→- **Evolutionary analysis**: [Evolutionary Analysis](#evolutionary-analysis)
   159→- **Specialized environments**: [Other Tools](#other-tools)
   160→
   161→> **💡 Tip**: New to virome analysis? Start with the [Quick Start Guide](#quick-start-guide) above for essential tool recommendations.
   162→
   163→---
   164→
   165→## Virus and Phage Identification
   166→
   167→### Metagenome Analysis
   168→
   169→- [Cenote-Taker 3](https://github.com/mtisza1/Cenote-Taker3) [v0.1.0, 2023] - Hallmark gene discovery, gene annotation, flanking host gene removal. [Linux/MacOS] [conda] [v0.1.0, 2023]
   170→- [Cenote-Taker 2](https://github.com/mtisza1/Cenote-Taker2) [v2.1.5, 2022] - Scans contigs for virus hallmark genes, removes flanking host DNA from prophages, makes annotated genome maps. [conda, pip] [v2.1.5, 2022]
   171→- [CoCoNet](https://github.com/Puumanamana/CoCoNet) [Updated: 03/2025] - Neural networks for viral contig identification. [pip] [Python]
   172→- [crassus](https://github.com/dcarrillox/CrassUS) [Updated: 04/2023] - Snakemake workflow for phage discovery. [conda] [Python]
   173→- [DBSCAN-SWA](https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/) [Updated: 12/2024] - DBSCAN clustering for phage identification. [Python]
   174→- [Deep6](https://github.com/janfelix/Deep6) [Updated: 03/2024] - Machine learning based virus identification. [Python]
   175→- [DeepVirFinder](https://github.com/jessieren/DeepVirFinder) [Updated: 03/2025] - Neural network approach for viral contig identification. [Python]
   176→- [DePhT](https://github.com/chg60/DEPhT) [Updated: 12/2024] - Deep-learning Phage Taxonomy for phage identification. [conda] [Python]
   177→- [FastViromeExplorer](https://code.vt.edu/saima5/FastViromeExplorer) - Detects viral sequences and predicts abundance by pseudoalignment of reads to a database. [Java]
   178→- [GenomePeek](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0663-4) - Taxonomic classification of multiple domains. [Python]
   179→- [hecatomb](https://github.com/shandley/hecatomb) [Updated: 01/2025] - Pipeline for virus identification from metagenomic data. [Nextflow]
   180→- [HoloVir](https://github.com/plaffy/HoloVir) [Updated: 01/2024] - Pipeline for taxonomic classification and gene function assignment. [Perl]
   181→- [INHERIT](https://github.com/Celestial-Bai/INHERIT) [Updated: 03/2025] - BERT embedding-based phage identification. [Python]
   182→- [INSaFLU-TELEVIR](https://github.com/INSaFLU/INSaFLU) [Updated: 01/2025] - Platform for virus identification and characterization. [Python]
   183→- [isling](https://github.com/szsctt/intvi_other-tools) [Updated: 08/2021] - Split read alignment for virus identification. [Python]
   184→- [Jaeger](https://github.com/Yasas1994/Jaeger) [Updated: 03/2025] - Phage identification in metagenomes. [Python]
   185→- [Jovian](https://github.com/DennisSchmitz/Jovian) [Updated: 01/2025] - Public health toolkit focused on human viruses. [Nextflow]
   186→- [LazyPipe](https://www.helsinki.fi/en/projects/lazypipe) - Taxonomic profiling and reference-based detection. [Nextflow]
   187→- [MARVEL](https://github.com/LaboratorioBioinformatica/MARVEL) [Updated: 02/2025] - Random forest classifier for phage identification (not for prophages). [Python]
   188→- [metaPhage](https://mattiapandolfovr.github.io/MetaPhage/) - Pipeline for phage and virus identification. [conda] [Nextflow]
   189→- [MetaPhinder](https://github.com/vanessajurtz/MetaPhinder) [Updated: 07/2024] - Integrates BLAST hits to multiple phage genomes to identify phage sequences. [Python]
   190→- [MetaPhlAn 4.1.0](https://github.com/biobakery/MetaPhlAn/releases/tag/4.1.0) [Updated: 03/2025] - Read mapping-based virus identification. [conda, pip] [Python]
   191→- [PhaBox](https://phage.ee.cityu.edu.hk/) - Integrates several phage tools: PhaMer, PhaTYP, PhaGCN, and CHERRY. [conda] [Python]
   192→- [Phage tools](https://github.com/sxh1136/Phage_tools) [Updated: 01/2024] - Collection of tools for predicting and identifying phage in metagenomes. [Python]
   193→- [PHAMB](https://github.com/RasmussenLab/phamb) [Updated: 02/2025] - Random forest based phage identification. [conda] [Python]
   194→- [phaMers](https://github.com/jondeaton/PhaMers) [Updated: 04/2023] - K-mer and machine learning phage identification. [Python]
   195→- [Phanta](https://github.com/bhattlab/phanta) [Updated: 03/2025] - K-mer read based classification via snakemake workflow. [yaml] [Python]
   196→- [PIGv](https://github.com/BenMinch/PIGv) [Updated: 12/2024] - Giant virus identification using Metabat binning, k-mer scoring, and marker genes. [source] [Python]
   197→- [PPR-Meta](https://github.com/zhenchengfang/PPR-Meta) [Updated: 03/2025] - Convolutional neural network for phage prediction. [Python]
   198→- [Prophage Tracer](https://academic.oup.com/nar/article/49/22/e128/6374144) - Split read alignment for prophage identification. [Python]
   199→- [Seeker](https://github.com/gussow/seeker) [Updated: 08/2024] - LSTM-based phage identification (not recommended for prophages). [pip] [Python]

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

   545→- [Recentrifuge](https://github.com/khyox/recentrifuge) [Updated: 02/2025] - Classification tool for novel sequences. [Python]
   546→- [VirSorter-DarkMatter](https://github.com/simroux/VirSorter) [Updated: 01/2025] - Extension focused on novel viral sequences. [Perl]
   547→
   548→---
   549→
   550→## Interactive Dashboard
   551→
   552→Explore our [Interactive Dashboard](https://shandley.github.io/awesome-virome/dashboard.html) to visualize tool relationships and adoption patterns in the virome analysis ecosystem.
   553→
   554→![Dashboard Preview](dashboard.png)
   555→
   556→The dashboard offers powerful visualizations to understand the virome analysis tool landscape:
   557→
   558→- **Tool Categorization Treemap**: Quickly see how tools are distributed across functional categories
   559→- **Interactive Network**: Discover relationships between tools, categories, and subcategories
   560→- **Tool Timeline**: Visualize the evolution of the virome analysis tool ecosystem
   561→- **Programming Languages**: Analyze technology trends across the tool collection
   562→
   563→[Launch Dashboard](https://shandley.github.io/awesome-virome/dashboard.html) | [Compare Tools](https://shandley.github.io/awesome-virome/comparison.html)
   564→
   565→## Tool Comparison Matrix
   566→
   567→Need to quickly compare different tools? Our [interactive comparison matrix](https://shandley.github.io/awesome-virome/comparison.html) allows you to:
   568→
   569→- Compare tools side-by-side with key metrics and features
   570→- Filter by category, language, maintenance status, and more
   571→- Sort by stars, citations, or update frequency
   572→- Export results to CSV or JSON for your analysis
   573→
   574→The matrix is designed to help researchers quickly evaluate and select the most appropriate tools for their workflows.
   575→
   576→[Open Comparison Matrix](https://shandley.github.io/awesome-virome/comparison.html)
   577→
   578→## Tool Selection Guide
   579→
   580→Not sure which tool to use? Our [interactive selection guide](https://shandley.github.io/awesome-virome/selection-guide.html) helps you navigate through the vast ecosystem of viral analysis tools:
   581→
   582→- Answer simple questions about your research needs
   583→- Follow a decision tree to narrow down tool options
   584→- Receive personalized tool recommendations
   585→- Learn about key features and requirements for each tool
   586→
   587→The guide is perfect for researchers new to virome analysis or those exploring unfamiliar analysis types.
   588→
   589→[Open Selection Guide](https://shandley.github.io/awesome-virome/selection-guide.html)
   590→
   591→## Introduction to Virome Analysis
   592→
   593→Virome analysis involves studying the collection of viruses (including bacteriophages) in a specific environment such as the human gut, soil, or oceans. These analyses typically include:
   594→
   595→1. Identifying viral sequences in metagenomic data
   596→2. Classifying viruses and predicting their hosts
   597→3. Assembling and annotating viral genomes
   598→4. Analyzing viral diversity and evolution
   599→5. Studying virus-host interactions and functional potential
   600→
   601→> **Note on Tool Availability**: This list contains tools developed over many years. Some tools may no longer be actively maintained or might have moved to new locations. We mark tools that are no longer available as [unavailable] and provide archive links when possible. If you find a broken link or know of a tool's new location, please submit a PR or issue.
   602→
   603→## Contributing
   604→
   605→Please feel free to [contribute](CONTRIBUTING.md)!
   606→
   607→This repository welcomes contributions from the community. Here's how you can help:
   608→
   609→1. **Add New Tools**: Submit entries for tools not yet included in the list
   610→2. **Update Information**: Help keep tool descriptions and links up to date
   611→3. **Report Issues**: Let us know about broken links or outdated information
   612→4. **Improve Documentation**: Suggest enhancements to the documentation
   613→5. **Fix Bugs**: Help resolve issues with the website or dashboard
   614→
   615→We provide standardized issue templates to make contributing easier:
   616→- **Tool Addition**: Template for suggesting new tools
   617→- **Tool Update**: Template for updating existing tool information
   618→- **Bug Report**: Template for reporting issues with the repository
   619→- **Feature Request**: Template for suggesting new features
   620→
   621→For more details, see our [contribution guidelines](CONTRIBUTING.md).
   622→
   623→## Repository Maintenance
   624→
   625→This repository uses a streamlined GitHub Actions workflow system to maintain data and deployments:
   626→
   627→1. **Automated Updates**: Weekly basic updates and monthly comprehensive metadata updates
   628→2. **Data Management**: All data is stored in `data.json` and displayed through GitHub Pages
   629→3. **Contribution Flow**: External contributors can propose changes via Pull Requests
   630→4. **API Access**: Programmatic access to the database via a [REST API](API.md)
   631→5. **Automated Changelog**: Monthly release notes documenting tool additions, updates, and removals
   632→
   633→For technical details, see the [workflow documentation](.github/workflows/README.md) and [view our release notes](https://github.com/shandley/awesome-virome/releases).
   634→
   635→## Enhanced Metadata
   636→
   637→This repository features an enhanced metadata collection system that enriches tool information with details from GitHub, GitLab, and Bitbucket repositories:
   638→
   639→- **Repository Statistics**: Star counts, forks, open issues, and watchers
   640→- **License Information**: License type and details for each tool
   641→- **Programming Languages**: Primary and secondary languages used
   642→- **Repository Topics/Tags**: Topic classifications from repository metadata
   643→- **Release Information**: Latest release version and date
   644→- **Creation & Update Dates**: When repositories were created and last updated

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

Todos have been modified successfully. Ensure that you continue to use the todo list to track your progress. Please proceed with the current tasks if applicable

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/README.md has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
    18→- Experienced scientists looking for specific tools
    19→- Developers building viral analysis workflows
    20→- Students learning computational virology
    21→
    22→**🚀 Key Features:**
    23→- Curated collection of 300+ tools across 8 major categories
    24→- Interactive dashboard with visualization and analytics
    25→- Tool comparison matrix with filtering and export
    26→- Automated metadata collection from GitHub/GitLab/Bitbucket
    27→- RESTful API for programmatic access
    28→- Weekly updates and quality assurance
    29→
    30→## 🌟 Explore Interactively
    31→
    32→Don't just read about tools - **explore them visually!** Our interactive web applications make discovering and comparing viral analysis tools fast and intuitive.
    33→
    34→### [📊 Interactive Dashboard](https://shandley.github.io/awesome-virome/dashboard.html)
    35→Visualize the entire virome analysis ecosystem at a glance:
    36→- **Tool Categorization Treemap** - See how 300+ tools are distributed across categories
    37→- **Interactive Network Graph** - Explore relationships between tools and categories
    38→- **Timeline Visualization** - Track the evolution of viral analysis tools over time
    39→- **Technology Trends** - Analyze programming language usage across the collection
    40→
    41→[**Launch Dashboard →**](https://shandley.github.io/awesome-virome/dashboard.html)
    42→
    43→### [⚖️ Tool Comparison Matrix](https://shandley.github.io/awesome-virome/comparison.html)
    44→Compare tools side-by-side to find the perfect fit:
    45→- **Multi-tool comparison** with key metrics and features
    46→- **Advanced filtering** by category, language, maintenance status
    47→- **Smart sorting** by stars, update frequency, or custom criteria
    48→- **Export capabilities** to CSV or JSON for further analysis
    49→
    50→[**Compare Tools →**](https://shandley.github.io/awesome-virome/comparison.html)
    51→
    52→### [🧭 Tool Selection Guide](https://shandley.github.io/awesome-virome/selection-guide.html)
    53→Get personalized recommendations through our interactive decision tree:
    54→- Answer simple questions about your research needs
    55→- Follow guided pathways to narrow down options
    56→- Receive tool recommendations tailored to your workflow
    57→- Learn key features and requirements for each suggestion
    58→
    59→[**Get Recommendations →**](https://shandley.github.io/awesome-virome/selection-guide.html)
    60→
    61→---
    62→
    63→## Introduction to Virome Analysis
    64→
    65→Virome analysis involves studying the collection of viruses (including bacteriophages) in a specific environment such as the human gut, soil, or oceans. These analyses typically include:
    66→
    67→1. Identifying viral sequences in metagenomic data
    68→2. Classifying viruses and predicting their hosts
    69→3. Assembling and annotating viral genomes
    70→4. Analyzing viral diversity and evolution
    71→5. Studying virus-host interactions and functional potential
    72→
    73→> **Note on Tool Availability**: This list contains tools developed over many years. Some tools may no longer be actively maintained or might have moved to new locations. We mark tools that are no longer available as [unavailable] and provide archive links when possible. If you find a broken link or know of a tool's new location, please submit a PR or issue.
    74→
    75→---
    76→
    77→## Quick Start Guide
    78→
    79→**New to virome analysis?** Here are the essential tools to get you started:
    80→
    81→| Analysis Step | Recommended Tools | Purpose |

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/README.md has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
    94→5. Taxonomic classification → [Taxonomy](#taxonomy)
    95→6. Host prediction → [Host Prediction](#host-prediction)
    96→7. Functional annotation → [Functional Analysis](#functional-analysis)
    97→
    98→**🎯 Quick Access:**
    99→- [**Explore Interactive Tools**](#-explore-interactively) ↑
   100→- [**Browse All Tools by Category**](#virus-and-phage-identification) ↓
   101→
   102→## Top Tools by Category
   103→
   104→Here are the most popular and well-maintained tools in each major category:

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   135→1. [AlphaFold-Multimer](https://github.com/deepmind/alphafold) (⭐ 13320) - Protein structure prediction
   136→2. [CovidMD](https://github.com/lammps/lammps) (⭐ 2365) - Molecular dynamics for COVID-19
   137→3. [BLAST+DIAMOND](https://github.com/bbuchfink/diamond) (⭐ 1114) - Fast sequence alignment
   138→
   139→## Contents
   140→
   141→### 🚀 Getting Started
   142→- [What is Awesome-Virome?](#what-is-awesome-virome)
   143→- [Explore Interactively](#-explore-interactively)
   144→- [Introduction to Virome Analysis](#introduction-to-virome-analysis)
   145→- [Quick Start Guide](#quick-start-guide)
   146→- [Top Tools by Category](#top-tools-by-category)
   147→
   148→### 🔧 Core Analysis Tools
   149→- [Virus and Phage Identification](#virus-and-phage-identification)
   150→  - [Metagenome Analysis](#metagenome-analysis)

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/README.md has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
   172→- [Sequence Analysis](#sequence-analysis)
   173→- [CRISPR Analysis](#crispr-analysis)
   174→- [Other Tools](#other-tools)
   175→
   176→### 🌐 Resources
   177→- [API Support](#api-support)
   178→
   179→### 📚 Project Information
   180→- [Contributing](#contributing)
   181→- [Repository Maintenance](#repository-maintenance)
   182→- [Acknowledgments](#acknowledgments)
   183→- [License](#license)
   184→

   184→
   185→---
   186→
   187→## Typical Workflows
   188→
   189→### Basic Virome Analysis Workflow:
   190→1. Quality control of metagenomic reads
   191→2. Assembly of contigs (e.g., SPAdes, MEGAHIT)
   192→3. Identification of viral contigs → [Virus and Phage Identification](#virus-and-phage-identification)
   193→4. Quality assessment → [Genome Analysis](#genome-analysis)
   194→5. Taxonomic classification → [Taxonomy](#taxonomy)
   195→6. Host prediction → [Host Prediction](#host-prediction)
   196→7. Functional annotation → [Functional Analysis](#functional-analysis)
   197→
   198→### Advanced Analysis Options:
   199→- **Strain reconstruction**: [Viral Strain Reconstruction](#viral-strain-reconstruction)
   200→- **Host-virus interactions**: [Interaction Analysis](#interaction-analysis)
   201→- **Evolutionary analysis**: [Evolutionary Analysis](#evolutionary-analysis)
   202→- **Specialized environments**: [Other Tools](#other-tools)
   203→
   204→> **💡 Tip**: New to virome analysis? Start with the [Quick Start Guide](#quick-start-guide) above for essential tool recommendations.
   205→
   206→---
   207→
   208→## Virus and Phage Identification
   209→
   210→### Metagenome Analysis
   211→
   212→- [Cenote-Taker 3](https://github.com/mtisza1/Cenote-Taker3) [v0.1.0, 2023] - Hallmark gene discovery, gene annotation, flanking host gene removal. [Linux/MacOS] [conda] [v0.1.0, 2023]
   213→- [Cenote-Taker 2](https://github.com/mtisza1/Cenote-Taker2) [v2.1.5, 2022] - Scans contigs for virus hallmark genes, removes flanking host DNA from prophages, makes annotated genome maps. [conda, pip] [v2.1.5, 2022]

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/README.md has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
   181→- [Repository Maintenance](#repository-maintenance)
   182→- [Acknowledgments](#acknowledgments)
   183→- [License](#license)
   184→
   185→---
   186→
   187→## Virus and Phage Identification
   188→
   189→### Metagenome Analysis
   190→
   191→- [Cenote-Taker 3](https://github.com/mtisza1/Cenote-Taker3) [v0.1.0, 2023] - Hallmark gene discovery, gene annotation, flanking host gene removal. [Linux/MacOS] [conda] [v0.1.0, 2023]

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572:## Interactive Dashboard

[Showing results with pagination = limit: 100, offset: 0]

   570→---
   571→
   572→## Interactive Dashboard
   573→
   574→Explore our [Interactive Dashboard](https://shandley.github.io/awesome-virome/dashboard.html) to visualize tool relationships and adoption patterns in the virome analysis ecosystem.
   575→
   576→![Dashboard Preview](dashboard.png)
   577→
   578→The dashboard offers powerful visualizations to understand the virome analysis tool landscape:
   579→
   580→- **Tool Categorization Treemap**: Quickly see how tools are distributed across functional categories
   581→- **Interactive Network**: Discover relationships between tools, categories, and subcategories
   582→- **Tool Timeline**: Visualize the evolution of the virome analysis tool ecosystem
   583→- **Programming Languages**: Analyze technology trends across the tool collection
   584→
   585→[Launch Dashboard](https://shandley.github.io/awesome-virome/dashboard.html) | [Compare Tools](https://shandley.github.io/awesome-virome/comparison.html)
   586→
   587→## Tool Comparison Matrix
   588→
   589→Need to quickly compare different tools? Our [interactive comparison matrix](https://shandley.github.io/awesome-virome/comparison.html) allows you to:
   590→
   591→- Compare tools side-by-side with key metrics and features
   592→- Filter by category, language, maintenance status, and more
   593→- Sort by stars, citations, or update frequency
   594→- Export results to CSV or JSON for your analysis
   595→
   596→The matrix is designed to help researchers quickly evaluate and select the most appropriate tools for their workflows.
   597→
   598→[Open Comparison Matrix](https://shandley.github.io/awesome-virome/comparison.html)
   599→
   600→## Tool Selection Guide
   601→
   602→Not sure which tool to use? Our [interactive selection guide](https://shandley.github.io/awesome-virome/selection-guide.html) helps you navigate through the vast ecosystem of viral analysis tools:
   603→
   604→- Answer simple questions about your research needs
   605→- Follow a decision tree to narrow down tool options
   606→- Receive personalized tool recommendations
   607→- Learn about key features and requirements for each tool
   608→
   609→The guide is perfect for researchers new to virome analysis or those exploring unfamiliar analysis types.
   610→
   611→[Open Selection Guide](https://shandley.github.io/awesome-virome/selection-guide.html)
   612→
   613→## Introduction to Virome Analysis
   614→
   615→Virome analysis involves studying the collection of viruses (including bacteriophages) in a specific environment such as the human gut, soil, or oceans. These analyses typically include:
   616→
   617→1. Identifying viral sequences in metagenomic data
   618→2. Classifying viruses and predicting their hosts
   619→3. Assembling and annotating viral genomes

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

   620→4. Analyzing viral diversity and evolution
   621→5. Studying virus-host interactions and functional potential
   622→
   623→> **Note on Tool Availability**: This list contains tools developed over many years. Some tools may no longer be actively maintained or might have moved to new locations. We mark tools that are no longer available as [unavailable] and provide archive links when possible. If you find a broken link or know of a tool's new location, please submit a PR or issue.
   624→
   625→## Contributing
   626→
   627→Please feel free to [contribute](CONTRIBUTING.md)!
   628→
   629→This repository welcomes contributions from the community. Here's how you can help:

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/README.md has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
   566→- [DarkVirome](https://web.archive.org/web/20210922051028/https://github.com/VerinaG/dark-virome) [unavailable] - Analysis of unclassified viral sequences. [Python]
   567→- [Recentrifuge](https://github.com/khyox/recentrifuge) [Updated: 02/2025] - Classification tool for novel sequences. [Python]
   568→- [VirSorter-DarkMatter](https://github.com/simroux/VirSorter) [Updated: 01/2025] - Extension focused on novel viral sequences. [Perl]
   569→
   570→---
   571→
   572→## Contributing
   573→
   574→Please feel free to [contribute](CONTRIBUTING.md)!
   575→
   576→This repository welcomes contributions from the community. Here's how you can help:

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     717 README.md

656:## Unique Features

[Showing results with pagination = limit: 100, offset: 0]

   656→## Unique Features
   657→
   658→Awesome-Virome offers several unique features that enhance its value as a resource for the viral bioinformatics community:
   659→
   660→### Interactive Visualizations
   661→- Dynamic network graph showing tool relationships and connections
   662→- Tool categorization treemap for understanding the ecosystem
   663→- Timeline visualization showing field development over time
   664→
   665→### Enhanced Metadata Collection
   666→- Automated metadata enrichment from GitHub, GitLab and Bitbucket
   667→- Detailed repository statistics including stars, forks, and languages
   668→- License information and release history tracking
   669→- Programming language distribution analysis
   670→
   671→### Community Contributions
   672→- Standardized issue templates for tool additions and updates
   673→- Automated workflows for data validation and site health checks
   674→- Detailed contribution guidelines for consistent data entry
   675→- Regular updates to ensure tool information remains current
   676→
   677→### Data Access Options
   678→- Web interface for browsing and searching tools
   679→- Interactive dashboard for visual exploration
   680→- RESTful API for programmatic access
   681→- Markdown files for simple text-based access
   682→
   683→---
   684→
   685→## License

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

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1 file changed, 51 insertions(+), 82 deletions(-)

To https://github.com/shandley/awesome-virome.git
   8ac6ff594..3623f081f  main -> main

Todos have been modified successfully. Ensure that you continue to use the todo list to track your progress. Please proceed with the current tasks if applicable

     1→<!DOCTYPE html>
     2→<html lang="en">
     3→<head>
     4→    <meta charset="UTF-8">
     5→    <meta name="viewport" content="width=device-width, initial-scale=1.0">
     6→    <meta http-equiv="Cache-Control" content="no-cache, no-store, must-revalidate">
     7→    <meta http-equiv="Pragma" content="no-cache">
     8→    <meta http-equiv="Expires" content="0">
     9→    <title>Awesome-Virome Dashboard</title>
    10→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/css/bootstrap.min.css">
    11→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.11.1/font/bootstrap-icons.css">
    12→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/datatables.net-bs5@1.13.6/css/dataTables.bootstrap5.min.css">
    13→    <style>
    14→        :root {
    15→            /* Modern virology-themed color palette */
    16→            --primary-color: #109b81; /* Teal green */
    17→            --primary-light: #6FC3BA;
    18→            --primary-dark: #097362;
    19→            --secondary-color: #2C4B7C; /* Deep blue */
    20→            --secondary-light: #557EBF;
    21→            --secondary-dark: #193152;
    22→            --accent-color: #9D5EB0; /* Purple for viruses */
    23→            --accent-light: #C89AD3;
    24→            --accent-dark: #6A3877;
    25→            --info-color: #3498db; /* Blue for info */
    26→            --success-color: #28a745; /* Green for success */
    27→            --warning-color: #ffc107; /* Yellow for warnings */
    28→            --danger-color: #e74c3c; /* Red for errors */
    29→            --light-bg: #f8f9fa;
    30→            --dark-bg: #1E293B; /* Dark slate blue */
    31→            --card-bg: #ffffff;
    32→            --card-bg-dark: #334155;
    33→            --card-shadow: 0 4px 6px rgba(0, 0, 0, 0.05);
    34→            --card-shadow-hover: 0 8px 15px rgba(0, 0, 0, 0.1);
    35→            --transition-speed: 0.3s;
    36→            --border-radius: 12px;
    37→            --section-padding: 2rem;
    38→            --card-spacing: 1.5rem;
    39→            --nav-height: 4rem;
    40→            
    41→            /* Category-specific colors */
    42→            --color-identification: #4682B4; /* Steel Blue */
    43→            --color-host: #6A5ACD; /* Slate Blue */
    44→            --color-genome: #20B2AA; /* Light Sea Green */
    45→            --color-taxonomy: #DB7093; /* Pale Violet Red */
    46→            --color-functional: #9370DB; /* Medium Purple */
    47→            --color-structural: #4169E1; /* Royal Blue */
    48→            --color-crispr: #FF6347; /* Tomato */
    49→            --color-database: #3CB371; /* Medium Sea Green */
    50→            --color-sequence: #1E90FF; /* Dodger Blue */
    51→            --color-visualization: #FF8C00; /* Dark Orange */
    52→            --color-other: #778899; /* Light Slate Gray */
    53→        }
    54→
    55→        body {
    56→            min-height: 100vh;
    57→            background-color: var(--light-bg);
    58→            color: #333;
    59→            font-family: 'Inter', system-ui, -apple-system, sans-serif;
    60→            padding-top: var(--nav-height);
    61→        }
    62→
    63→        [data-theme="dark"] {
    64→            background-color: var(--dark-bg);
    65→            color: #f8f9fa;
    66→        }
    67→
    68→        /* Navbar styling */
    69→        .navbar {
    70→            background-color: var(--secondary-color);
    71→            box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1);
    72→            height: var(--nav-height);
    73→            z-index: 1030;
    74→        }
    75→
    76→        .navbar-brand {
    77→            font-weight: 700;
    78→            color: white !important;
    79→        }
    80→
    81→        .navbar-brand span {
    82→            color: var(--primary-light);
    83→        }
    84→
    85→        .nav-link {
    86→            position: relative;
    87→            padding: 0.5rem 1rem;
    88→            color: rgba(255, 255, 255, 0.9) !important;
    89→            font-weight: 500;
    90→            transition: color var(--transition-speed);
    91→        }
    92→
    93→        .nav-link:hover, .nav-link:focus {
    94→            color: #ffffff !important;
    95→        }
    96→
    97→        .nav-link.active {
    98→            color: #ffffff !important;
    99→        }
   100→

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

   360→            height: 100%;
   361→        }
   362→    </style>
   363→</head>
   364→<body>
   365→    <!-- Navbar -->
   366→    <nav class="navbar navbar-expand-lg navbar-dark fixed-top">
   367→        <div class="container-fluid">
   368→            <a class="navbar-brand" href="index.html">Awesome-<span>Virome</span></a>
   369→            <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarNav" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation">
   370→                <span class="navbar-toggler-icon"></span>
   371→            </button>
   372→            <div class="collapse navbar-collapse" id="navbarNav">
   373→                <ul class="navbar-nav me-auto mb-2 mb-lg-0">
   374→                    <li class="nav-item">
   375→                        <a class="nav-link active" href="dashboard.html">Dashboard</a>
   376→                    </li>
   377→                    <li class="nav-item">
   378→                        <a class="nav-link" href="comparison.html">Tool Comparison</a>
   379→                    </li>
   380→                    <li class="nav-item">
   381→                        <a class="nav-link" href="selection-guide.html">Selection Guide</a>
   382→                    </li>
   383→                </ul>
   384→                <div class="d-flex align-items-center">
   385→                    <div class="theme-toggle me-3" id="theme-toggle">
   386→                        <i class="bi bi-moon-fill"></i>
   387→                    </div>
   388→                    <a href="https://github.com/shandley/awesome-virome" class="btn btn-outline-light" target="_blank">
   389→                        <i class="bi bi-github me-1"></i> GitHub
   390→                    </a>
   391→                </div>
   392→            </div>
   393→        </div>
   394→    </nav>
   395→
   396→    <!-- Dashboard Container -->
   397→    <div class="dashboard-container container-fluid">
   398→        <!-- Introduction -->
   399→        <div class="row mb-4">

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

-rw-r--r--@ 1 scotthandley  staff  97513 May  4  2025 index.html

     1→<!DOCTYPE html>
     2→<html lang="en">
     3→<head>
     4→    <meta charset="UTF-8">
     5→    <meta name="viewport" content="width=device-width, initial-scale=1.0">
     6→    <meta http-equiv="Cache-Control" content="no-cache, no-store, must-revalidate">
     7→    <meta http-equiv="Pragma" content="no-cache">
     8→    <meta http-equiv="Expires" content="0">
     9→    <title>Awesome-Virome Dashboard</title>
    10→    <meta http-equiv="refresh" content="0;url=dashboard.html">
    11→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/css/bootstrap.min.css">
    12→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.11.1/font/bootstrap-icons.css">
    13→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/datatables.net-bs5@1.13.6/css/dataTables.bootstrap5.min.css">
    14→    <style>
    15→        :root {
    16→            /* Modern virology-themed color palette */
    17→            --primary-color: #109b81; /* Teal green */
    18→            --primary-light: #6FC3BA;
    19→            --primary-dark: #097362;
    20→            --secondary-color: #2C4B7C; /* Deep blue */
    21→            --secondary-light: #557EBF;
    22→            --secondary-dark: #193152;
    23→            --accent-color: #9D5EB0; /* Purple for viruses */
    24→            --accent-light: #C89AD3;
    25→            --accent-dark: #6A3877;
    26→            --info-color: #3498db; /* Blue for info */
    27→            --success-color: #28a745; /* Green for success */
    28→            --warning-color: #ffc107; /* Yellow for warnings */
    29→            --danger-color: #e74c3c; /* Red for errors */
    30→            --light-bg: #f8f9fa;
    31→            --dark-bg: #1E293B; /* Dark slate blue */
    32→            --card-bg: #ffffff;
    33→            --card-bg-dark: #334155;
    34→            --card-shadow: 0 4px 6px rgba(0, 0, 0, 0.05);
    35→            --card-shadow-hover: 0 8px 15px rgba(0, 0, 0, 0.1);
    36→            --transition-speed: 0.3s;
    37→            --border-radius: 12px;
    38→            --section-padding: 2rem;
    39→            --card-spacing: 1.5rem;
    40→            --nav-height: 4rem;
    41→            
    42→            /* Category-specific colors */
    43→            --color-identification: #4682B4; /* Steel Blue */
    44→            --color-host: #6A5ACD; /* Slate Blue */
    45→            --color-genome: #20B2AA; /* Light Sea Green */
    46→            --color-taxonomy: #DB7093; /* Pale Violet Red */
    47→            --color-functional: #9370DB; /* Medium Purple */
    48→            --color-structural: #4169E1; /* Royal Blue */
    49→            --color-crispr: #FF6347; /* Tomato */
    50→            --color-database: #3CB371; /* Medium Sea Green */

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

Todos have been modified successfully. Ensure that you continue to use the todo list to track your progress. Please proceed with the current tasks if applicable

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/index.html has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
     1→<!DOCTYPE html>
     2→<html lang="en">
     3→<head>
     4→    <meta charset="UTF-8">
     5→    <meta name="viewport" content="width=device-width, initial-scale=1.0">
     6→    <meta http-equiv="Cache-Control" content="no-cache, no-store, must-revalidate">
     7→    <meta http-equiv="Pragma" content="no-cache">
     8→    <meta http-equiv="Expires" content="0">
     9→    <title>Awesome-Virome - Curated Viral Analysis Tools</title>
    10→    <meta name="description" content="A comprehensive, curated database of 300+ software tools for virome analysis">
    11→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/css/bootstrap.min.css">
    12→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.11.1/font/bootstrap-icons.css">
    13→    <style>
    14→        :root {
    15→            /* Modern virology-themed color palette */
    16→            --primary-color: #109b81;
    17→            --primary-light: #6FC3BA;
    18→            --primary-dark: #097362;
    19→            --secondary-color: #2C4B7C;
    20→            --secondary-light: #557EBF;
    21→            --secondary-dark: #193152;
    22→            --accent-color: #9D5EB0;
    23→            --accent-light: #C89AD3;
    24→            --accent-dark: #6A3877;
    25→            --light-bg: #f8f9fa;
    26→            --dark-bg: #1E293B;
    27→            --card-bg: #ffffff;
    28→            --card-shadow: 0 4px 6px rgba(0, 0, 0, 0.05);
    29→            --card-shadow-hover: 0 8px 15px rgba(0, 0, 0, 0.1);
    30→            --transition-speed: 0.3s;
    31→            --border-radius: 12px;
    32→            --nav-height: 4rem;
    33→        }
    34→
    35→        body {
    36→            min-height: 100vh;
    37→            background-color: var(--light-bg);
    38→            color: #333;
    39→            font-family: 'Inter', system-ui, -apple-system, sans-serif;
    40→            padding-top: var(--nav-height);
    41→        }
    42→
    43→        /* Navbar */
    44→        .navbar {
    45→            background-color: var(--secondary-color);
    46→            box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1);
    47→            height: var(--nav-height);
    48→            z-index: 1030;
    49→        }
    50→
    51→        .navbar-brand {
    52→            font-weight: 700;
    53→            color: white !important;
    54→            font-size: 1.5rem;
    55→        }
    56→
    57→        .navbar-brand span {
    58→            color: var(--primary-light);
    59→        }
    60→
    61→        .nav-link {
    62→            color: rgba(255, 255, 255, 0.9) !important;
    63→            font-weight: 500;
    64→            transition: color var(--transition-speed);
    65→            padding: 0.5rem 1rem;
    66→        }
    67→
    68→        .nav-link:hover {
    69→            color: #ffffff !important;
    70→        }
    71→
    72→        /* Hero Section */
    73→        .hero {
    74→            background: linear-gradient(135deg, var(--secondary-dark) 0%, var(--secondary-color) 50%, var(--primary-dark) 100%);
    75→            color: white;
    76→            padding: 5rem 0;
    77→            text-align: center;
    78→            position: relative;
    79→            overflow: hidden;
    80→        }
    81→
    82→        .hero::before {
    83→            content: '';
    84→            position: absolute;
    85→            top: 0;
    86→            left: 0;
    87→            right: 0;
    88→            bottom: 0;
    89→            background-image: url('awesome-virome-hex.png');
    90→            background-size: 200px;
    91→            background-position: center;
    92→            background-repeat: no-repeat;
    93→            opacity: 0.1;
    94→            pointer-events: none;
    95→        }
    96→
    97→        .hero h1 {
    98→            font-size: 3.5rem;
    99→            font-weight: 800;
   100→            margin-bottom: 1.5rem;
   101→            text-shadow: 2px 2px 4px rgba(0, 0, 0, 0.3);
   102→        }
   103→
   104→        .hero .lead {
   105→            font-size: 1.4rem;
   106→            margin-bottom: 2rem;
   107→            opacity: 0.95;
   108→        }
   109→
   110→        .hero-stats {
   111→            display: flex;
   112→            justify-content: center;
   113→            gap: 3rem;
   114→            margin: 3rem 0 2rem;
   115→            flex-wrap: wrap;
   116→        }
   117→
   118→        .stat-item {
   119→            text-align: center;
   120→        }
   121→
   122→        .stat-number {
   123→            font-size: 3rem;
   124→            font-weight: 800;
   125→            color: var(--primary-light);
   126→            line-height: 1;
   127→        }
   128→
   129→        .stat-label {
   130→            font-size: 1rem;
   131→            opacity: 0.9;
   132→            margin-top: 0.5rem;
   133→        }
   134→
   135→        /* Tool Cards */
   136→        .tool-card {
   137→            background: var(--card-bg);
   138→            border-radius: var(--border-radius);
   139→            padding: 2rem;
   140→            box-shadow: var(--card-shadow);
   141→            transition: all var(--transition-speed);
   142→            height: 100%;
   143→            border: none;
   144→            text-decoration: none;
   145→            display: block;
   146→            color: inherit;
   147→        }
   148→
   149→        .tool-card:hover {
   150→            box-shadow: var(--card-shadow-hover);
   151→            transform: translateY(-5px);
   152→            text-decoration: none;
   153→            color: inherit;
   154→        }
   155→
   156→        .tool-icon {
   157→            font-size: 3rem;
   158→            color: var(--primary-color);
   159→            margin-bottom: 1rem;
   160→        }
   161→
   162→        .tool-card h3 {
   163→            color: var(--secondary-color);
   164→            font-weight: 700;
   165→            margin-bottom: 1rem;
   166→            font-size: 1.5rem;
   167→        }
   168→
   169→        .tool-card p {
   170→            color: #666;
   171→            margin-bottom: 1rem;
   172→            line-height: 1.6;
   173→        }
   174→
   175→        .tool-card ul {
   176→            list-style: none;
   177→            padding: 0;
   178→            margin: 0;
   179→        }
   180→
   181→        .tool-card li {
   182→            padding: 0.5rem 0;
   183→            color: #666;
   184→            font-size: 0.95rem;
   185→        }
   186→
   187→        .tool-card li i {
   188→            color: var(--primary-color);
   189→            margin-right: 0.5rem;
   190→        }
   191→
   192→        .btn-hero {
   193→            padding: 0.875rem 2rem;
   194→            font-size: 1.1rem;
   195→            font-weight: 600;
   196→            border-radius: 8px;
   197→            transition: all var(--transition-speed);
   198→        }
   199→
   200→        .btn-primary-custom {
   201→            background-color: var(--primary-color);
   202→            border-color: var(--primary-color);
   203→            color: white;
   204→        }
   205→
   206→        .btn-primary-custom:hover {
   207→            background-color: var(--primary-dark);
   208→            border-color: var(--primary-dark);
   209→            transform: translateY(-2px);
   210→            box-shadow: 0 4px 12px rgba(16, 155, 129, 0.3);
   211→        }
   212→
   213→        .btn-outline-custom {
   214→            border: 2px solid white;
   215→            color: white;
   216→        }
   217→
   218→        .btn-outline-custom:hover {
   219→            background-color: white;
   220→            color: var(--secondary-color);
   221→        }
   222→
   223→        /* Features Section */
   224→        .features-section {
   225→            padding: 4rem 0;
   226→            background-color: white;
   227→        }
   228→
   229→        .feature-item {
   230→            text-align: center;
   231→            padding: 2rem;
   232→        }
   233→
   234→        .feature-icon {
   235→            font-size: 2.5rem;
   236→            color: var(--accent-color);
   237→            margin-bottom: 1rem;
   238→        }
   239→
   240→        .feature-item h4 {
   241→            color: var(--secondary-color);
   242→            font-weight: 600;
   243→            margin-bottom: 1rem;
   244→        }
   245→
   246→        .feature-item p {
   247→            color: #666;
   248→            line-height: 1.6;
   249→        }
   250→
   251→        /* CTA Section */
   252→        .cta-section {
   253→            background: linear-gradient(135deg, var(--accent-color) 0%, var(--accent-dark) 100%);
   254→            color: white;
   255→            padding: 4rem 0;
   256→            text-align: center;
   257→        }
   258→
   259→        .cta-section h2 {
   260→            font-size: 2.5rem;
   261→            font-weight: 700;
   262→            margin-bottom: 1.5rem;
   263→        }
   264→
   265→        .cta-section p {
   266→            font-size: 1.2rem;
   267→            margin-bottom: 2rem;
   268→            opacity: 0.95;
   269→        }
   270→
   271→        /* Footer */
   272→        .footer {
   273→            background-color: var(--secondary-dark);
   274→            color: rgba(255, 255, 255, 0.8);
   275→            padding: 2rem 0;
   276→            text-align: center;
   277→        }
   278→
   279→        .footer a {
   280→            color: var(--primary-light);
   281→            text-decoration: none;
   282→        }
   283→
   284→        .footer a:hover {
   285→            color: white;
   286→        }
   287→
   288→        /* Responsive */
   289→        @media (max-width: 768px) {
   290→            .hero h1 {
   291→                font-size: 2.5rem;
   292→            }
   293→
   294→            .hero .lead {
   295→                font-size: 1.1rem;
   296→            }
   297→
   298→            .stat-number {
   299→                font-size: 2rem;
   300→            }
   301→
   302→            .hero-stats {
   303→                gap: 1.5rem;
   304→            }
   305→        }
   306→    </style>
   307→</head>
   308→<body>
   309→    <!-- Navbar -->
   310→    <nav class="navbar navbar-expand-lg navbar-dark fixed-top">
   311→        <div class="container">
   312→            <a class="navbar-brand" href="index.html">Awesome-<span>Virome</span></a>
   313→            <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarNav">
   314→                <span class="navbar-toggler-icon"></span>
   315→            </button>
   316→            <div class="collapse navbar-collapse" id="navbarNav">
   317→                <ul class="navbar-nav ms-auto">
   318→                    <li class="nav-item">
   319→                        <a class="nav-link" href="dashboard.html">Dashboard</a>
   320→                    </li>
   321→                    <li class="nav-item">
   322→                        <a class="nav-link" href="comparison.html">Comparison</a>
   323→                    </li>
   324→                    <li class="nav-item">
   325→                        <a class="nav-link" href="selection-guide.html">Selection Guide</a>
   326→                    </li>
   327→                    <li class="nav-item">
   328→                        <a class="nav-link" href="https://github.com/shandley/awesome-virome">
   329→                            <i class="bi bi-github"></i> GitHub
   330→                        </a>
   331→                    </li>
   332→                </ul>
   333→            </div>
   334→        </div>
   335→    </nav>
   336→
   337→    <!-- Hero Section -->
   338→    <section class="hero">
   339→        <div class="container">
   340→            <h1>Awesome-Virome</h1>
   341→            <p class="lead">A comprehensive, curated database of software tools for virome analysis</p>
   342→
   343→            <div class="hero-stats">
   344→                <div class="stat-item">
   345→                    <div class="stat-number">300+</div>
   346→                    <div class="stat-label">Curated Tools</div>
   347→                </div>
   348→                <div class="stat-item">
   349→                    <div class="stat-number">8</div>
   350→                    <div class="stat-label">Major Categories</div>
   351→                </div>
   352→                <div class="stat-item">
   353→                    <div class="stat-number">164</div>
   354→                    <div class="stat-label">Active Repositories</div>
   355→                </div>
   356→            </div>
   357→
   358→            <div class="mt-4">
   359→                <a href="dashboard.html" class="btn btn-primary-custom btn-hero me-3">
   360→                    <i class="bi bi-bar-chart-fill me-2"></i>Explore Dashboard
   361→                </a>
   362→                <a href="https://github.com/shandley/awesome-virome/blob/main/README.md" class="btn btn-outline-custom btn-hero">
   363→                    <i class="bi bi-book me-2"></i>Browse Tools
   364→                </a>
   365→            </div>
   366→        </div>
   367→    </section>
   368→
   369→    <!-- Interactive Tools Section -->
   370→    <section class="py-5">
   371→        <div class="container">
   372→            <div class="text-center mb-5">
   373→                <h2 class="display-5 fw-bold mb-3" style="color: var(--secondary-color);">Explore Interactively</h2>
   374→                <p class="lead text-muted">Discover and compare viral analysis tools with our interactive web applications</p>
   375→            </div>
   376→
   377→            <div class="row g-4">
   378→                <div class="col-md-4">
   379→                    <a href="dashboard.html" class="tool-card">
   380→                        <div class="tool-icon">
   381→                            <i class="bi bi-graph-up-arrow"></i>
   382→                        </div>
   383→                        <h3>Interactive Dashboard</h3>
   384→                        <p>Visualize the entire virome analysis ecosystem at a glance</p>
   385→                        <ul>
   386→                            <li><i class="bi bi-check-circle-fill"></i>Tool categorization treemap</li>
   387→                            <li><i class="bi bi-check-circle-fill"></i>Interactive network graph</li>
   388→                            <li><i class="bi bi-check-circle-fill"></i>Timeline visualization</li>
   389→                            <li><i class="bi bi-check-circle-fill"></i>Technology trends analysis</li>
   390→                        </ul>
   391→                    </a>
   392→                </div>
   393→
   394→                <div class="col-md-4">
   395→                    <a href="comparison.html" class="tool-card">
   396→                        <div class="tool-icon">
   397→                            <i class="bi bi-columns-gap"></i>
   398→                        </div>
   399→                        <h3>Tool Comparison</h3>
   400→                        <p>Compare tools side-by-side to find the perfect fit for your workflow</p>
   401→                        <ul>
   402→                            <li><i class="bi bi-check-circle-fill"></i>Multi-tool comparison</li>
   403→                            <li><i class="bi bi-check-circle-fill"></i>Advanced filtering options</li>
   404→                            <li><i class="bi bi-check-circle-fill"></i>Smart sorting capabilities</li>
   405→                            <li><i class="bi bi-check-circle-fill"></i>Export to CSV/JSON</li>
   406→                        </ul>
   407→                    </a>
   408→                </div>
   409→
   410→                <div class="col-md-4">
   411→                    <a href="selection-guide.html" class="tool-card">
   412→                        <div class="tool-icon">
   413→                            <i class="bi bi-compass"></i>
   414→                        </div>
   415→                        <h3>Selection Guide</h3>
   416→                        <p>Get personalized recommendations through our interactive decision tree</p>
   417→                        <ul>
   418→                            <li><i class="bi bi-check-circle-fill"></i>Simple questionnaire</li>
   419→                            <li><i class="bi bi-check-circle-fill"></i>Guided pathways</li>
   420→                            <li><i class="bi bi-check-circle-fill"></i>Tailored recommendations</li>
   421→                            <li><i class="bi bi-check-circle-fill"></i>Feature explanations</li>
   422→                        </ul>
   423→                    </a>
   424→                </div>
   425→            </div>
   426→        </div>
   427→    </section>
   428→
   429→    <!-- Features Section -->
   430→    <section class="features-section">
   431→        <div class="container">
   432→            <div class="text-center mb-5">
   433→                <h2 class="display-5 fw-bold mb-3" style="color: var(--secondary-color);">Why Awesome-Virome?</h2>
   434→            </div>
   435→
   436→            <div class="row g-4">
   437→                <div class="col-md-3">
   438→                    <div class="feature-item">
   439→                        <div class="feature-icon">
   440→                            <i class="bi bi-award"></i>
   441→                        </div>
   442→                        <h4>Curated & Quality-Checked</h4>
   443→                        <p>Every tool is carefully reviewed and categorized by viral bioinformatics experts</p>
   444→                    </div>
   445→                </div>
   446→
   447→                <div class="col-md-3">
   448→                    <div class="feature-item">
   449→                        <div class="feature-icon">
   450→                            <i class="bi bi-arrow-repeat"></i>
   451→                        </div>
   452→                        <h4>Regularly Updated</h4>
   453→                        <p>Weekly automated updates ensure tool metadata stays current and accurate</p>
   454→                    </div>
   455→                </div>
   456→
   457→                <div class="col-md-3">
   458→                    <div class="feature-item">
   459→                        <div class="feature-icon">
   460→                            <i class="bi bi-code-square"></i>
   461→                        </div>
   462→                        <h4>API Access</h4>
   463→                        <p>RESTful API for programmatic access to the entire database</p>
   464→                    </div>
   465→                </div>
   466→
   467→                <div class="col-md-3">
   468→                    <div class="feature-item">
   469→                        <div class="feature-icon">
   470→                            <i class="bi bi-people"></i>
   471→                        </div>
   472→                        <h4>Community-Driven</h4>
   473→                        <p>Open to contributions from researchers worldwide through GitHub</p>
   474→                    </div>
   475→                </div>
   476→            </div>
   477→        </div>
   478→    </section>
   479→
   480→    <!-- Call to Action -->
   481→    <section class="cta-section">
   482→        <div class="container">
   483→            <h2>Ready to Start Your Virome Analysis?</h2>
   484→            <p>Explore 300+ tools, compare options, and find the perfect fit for your research</p>
   485→            <div class="mt-4">
   486→                <a href="dashboard.html" class="btn btn-light btn-lg me-3">
   487→                    <i class="bi bi-bar-chart-fill me-2"></i>Launch Dashboard
   488→                </a>
   489→                <a href="https://github.com/shandley/awesome-virome" class="btn btn-outline-light btn-lg">
   490→                    <i class="bi bi-github me-2"></i>View on GitHub
   491→                </a>
   492→            </div>
   493→        </div>
   494→    </section>
   495→
   496→    <!-- Footer -->
   497→    <footer class="footer">
   498→        <div class="container">
   499→            <p class="mb-2">
   500→                <strong>Awesome-Virome</strong> - A curated database of viral analysis tools
   501→            </p>
   502→            <p class="mb-0">
   503→                Maintained by <a href="https://github.com/shandley">Scott Handley</a> and contributors |
   504→                Licensed under <a href="https://github.com/shandley/awesome-virome/blob/main/LICENSE">MIT</a>
   505→            </p>
   506→        </div>
   507→    </footer>
   508→
   509→    <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/js/bootstrap.bundle.min.js"></script>
   510→</body>
   511→</html>
   512→

Todos have been modified successfully. Ensure that you continue to use the todo list to track your progress. Please proceed with the current tasks if applicable

1 file changed, 374 insertions(+), 2003 deletions(-)

To https://github.com/shandley/awesome-virome.git
   3623f081f..f8da16475  main -> main

Todos have been modified successfully. Ensure that you continue to use the todo list to track your progress. Please proceed with the current tasks if applicable

-rw-r--r--@   1 scotthandley  staff     9514 May  4  2025 API.md
-rw-r--r--@   1 scotthandley  staff     4614 Sep 18 20:27 CITATION_WORKFLOWS.md
-rw-r--r--@   1 scotthandley  staff     3117 Nov 29 14:57 CLAUDE.md
-rw-r--r--@   1 scotthandley  staff    56299 May  4  2025 comparison.html
-rw-r--r--@   1 scotthandley  staff     4392 May  4  2025 CONTRIBUTING.md
-rw-r--r--@   1 scotthandley  staff    95941 Nov 29 15:51 dashboard.html
-rw-r--r--@   1 scotthandley  staff     2968 May  4  2025 DASHBOARD.md
-rw-r--r--@   1 scotthandley  staff     2646 May  4  2025 index_redirect.html
-rw-r--r--@   1 scotthandley  staff    17365 Nov 29 16:04 index.html
-rw-r--r--@   1 scotthandley  staff     2189 May  4  2025 landing-page.html
-rw-r--r--@   1 scotthandley  staff    52196 Nov 29 16:00 README.md
-rw-r--r--@   1 scotthandley  staff     2110 May  4  2025 redirect.html
-rw-r--r--@   1 scotthandley  staff    81503 May  4  2025 selection-guide.html
-rw-r--r--@   1 scotthandley  staff     2100 May  4  2025 SITE_DEPLOYMENT.md
-rw-r--r--@   1 scotthandley  staff    10324 May  4  2025 starred_repos.md
-rw-r--r--@   1 scotthandley  staff     1495 May  4  2025 unavailable_repos.md

     1→<!DOCTYPE html>
     2→<html lang="en">
     3→<head>
     4→    <meta charset="UTF-8">
     5→    <meta name="viewport" content="width=device-width, initial-scale=1.0">
     6→    <title>Awesome-Virome</title>
     7→    <style>
     8→        body {
     9→            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Open Sans', 'Helvetica Neue', sans-serif;
    10→            line-height: 1.6;
    11→            color: #333;
    12→            max-width: 800px;
    13→            margin: 0 auto;
    14→            padding: 2rem;
    15→            text-align: center;
    16→        }
    17→        .logo {
    18→            max-width: 150px;
    19→            margin-bottom: 2rem;
    20→        }
    21→        h1 {
    22→            color: #2C4B7C;
    23→            margin-bottom: 1rem;
    24→        }
    25→        p {
    26→            margin-bottom: 2rem;
    27→            font-size: 1.1rem;
    28→        }
    29→        .buttons {
    30→            display: flex;
    31→            justify-content: center;
    32→            gap: 1rem;
    33→            flex-wrap: wrap;
    34→        }
    35→        .button {
    36→            display: inline-block;
    37→            background-color: #109b81;
    38→            color: white;
    39→            text-decoration: none;
    40→            padding: 1rem 2rem;
    41→            border-radius: 8px;
    42→            font-weight: 600;
    43→            transition: transform 0.2s, background-color 0.2s;
    44→        }
    45→        .button:hover {
    46→            background-color: #097362;
    47→            transform: translateY(-3px);
    48→        }
    49→        .button.secondary {
    50→            background-color: #2C4B7C;
    51→        }
    52→        .button.secondary:hover {
    53→            background-color: #193152;
    54→        }
    55→        .github-link {
    56→            margin-top: 3rem;
    57→            display: block;
    58→            color: #666;
    59→        }
    60→    </style>
    61→</head>
    62→<body>
    63→    <img src="awesome-virome-hex.png" alt="Awesome-Virome Logo" class="logo">
    64→    <h1>Welcome to Awesome-Virome</h1>
    65→    <p>A curated collection of virology bioinformatics tools and resources</p>
    66→    
    67→    <div class="buttons">
    68→        <a href="dashboard.html" class="button">Interactive Dashboard</a>
    69→        <a href="1.0.0/" class="button secondary">Documentation</a>
    70→    </div>
    71→    
    72→    <a href="https://github.com/shandley/awesome-virome" class="github-link" target="_blank">View on GitHub</a>
    73→</body>
    74→</html>

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

-rw-r--r--@ 1 scotthandley  staff   1428 May  6  2025 .github/workflows/auto-fix-dois.yml
-rw-r--r--@ 1 scotthandley  staff  11239 May  4  2025 .github/workflows/automated-changelog.yml
-rw-r--r--@ 1 scotthandley  staff  20338 May  4  2025 .github/workflows/broken-link-checker.yml
-rw-r--r--@ 1 scotthandley  staff   3610 May  4  2025 .github/workflows/cache-maintenance.yml
-rw-r--r--@ 1 scotthandley  staff   3283 May  4  2025 .github/workflows/contributor-suggestion.yml
-rw-r--r--@ 1 scotthandley  staff   2072 May  6  2025 .github/workflows/dashboard-update-workflow.yml
-rw-r--r--@ 1 scotthandley  staff   1438 May  6  2025 .github/workflows/fix-dois.yml
-rw-r--r--@ 1 scotthandley  staff   2558 May  6  2025 .github/workflows/pubmed-citations.yml
-rw-r--r--@ 1 scotthandley  staff  25104 May  4  2025 .github/workflows/repository-health-metrics.yml
-rw-r--r--@ 1 scotthandley  staff   1725 May  5  2025 .github/workflows/simplified-pages-deploy.yml
-rw-r--r--@ 1 scotthandley  staff   5727 Nov 29 15:52 .github/workflows/simplified-update-workflow.yml
-rw-r--r--@ 1 scotthandley  staff   4271 May  4  2025 .github/workflows/site-health-check.yml
-rw-r--r--@ 1 scotthandley  staff   2697 May  4  2025 .github/workflows/unified-pages-deploy.yml
-rw-r--r--@ 1 scotthandley  staff   1484 May  6  2025 .github/workflows/update-dashboard-data.yml
-rw-r--r--@ 1 scotthandley  staff  17523 May  4  2025 .github/workflows/validate-contribution.yml

     1→name: Deploy GitHub Pages
     2→
     3→on:
     4→  push:
     5→    branches: [ main ]
     6→    paths:
     7→      - 'data.json'
     8→      - 'impact_data.json'
     9→      - '*.html'
    10→      - 'metadata/**'
    11→      - 'reports/**'
    12→      - 'js/**'
    13→  workflow_dispatch:
    14→
    15→permissions:
    16→  contents: read
    17→  pages: write
    18→  id-token: write
    19→
    20→jobs:
    21→  deploy:
    22→    environment:
    23→      name: github-pages
    24→      url: ${{ steps.deployment.outputs.page_url }}
    25→    runs-on: ubuntu-latest
    26→    steps:
    27→      - name: Checkout
    28→        uses: actions/checkout@v4
    29→      
    30→      - name: Setup Pages
    31→        uses: actions/configure-pages@v4
    32→        
    33→      # Cache deployed pages to speed up deployment
    34→      - name: Cache Pages artifacts
    35→        uses: actions/cache@v4
    36→        with:
    37→          path: |
    38→            _site
    39→            .jekyll-cache
    40→          key: ${{ runner.os }}-pages-${{ hashFiles('data.json', 'impact_data.json', 'index.html') }}
    41→          restore-keys: |
    42→            ${{ runner.os }}-pages-
    43→      
    44→      - name: Debug citation data
    45→        run: |
    46→          echo "Checking impact_data.json content:"
    47→          jq '.tools | length' impact_data.json
    48→          echo "First few tools:"
    49→          jq '.tools | .[:5] | .[] | .name' impact_data.json
    50→      
    51→      - name: Generate visualization assets
    52→        run: |
    53→          # If you have any scripts that generate charts or other visualization assets
    54→          # based on data.json, you would run them here
    55→          
    56→          # Example (uncomment if needed):
    57→          # python scripts/generate_visualization_assets.py
    58→      
    59→      - name: Upload artifact
    60→        uses: actions/upload-pages-artifact@v3
    61→        with:
    62→          path: '.'
    63→      
    64→      - name: Deploy to GitHub Pages
    65→        id: deployment
    66→        uses: actions/deploy-pages@v4

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

f8da16475 Phase 3 Complete: Create professional landing page
841903c07 Fix navigation links to use standard filenames
4dc18b4a5 Implement D3.js network graph and Chart.js analytics visualizations
64c2b9af0 added the ability to check crossref when semantic scholar can not find citations
e0de29307 fixed DOI formatting

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/landing-page.html has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
     1→<!DOCTYPE html>
     2→<html lang="en">
     3→<head>
     4→    <meta charset="UTF-8">
     5→    <meta name="viewport" content="width=device-width, initial-scale=1.0">
     6→    <title>Awesome-Virome - Curated Viral Analysis Tools</title>
     7→    <meta name="description" content="A comprehensive, curated database of 300+ software tools for virome analysis">
     8→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/css/bootstrap.min.css">
     9→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.11.1/font/bootstrap-icons.css">
    10→    <style>
    11→        :root {
    12→            --primary-color: #109b81;
    13→            --primary-light: #6FC3BA;
    14→            --primary-dark: #097362;
    15→            --secondary-color: #2C4B7C;
    16→            --secondary-dark: #193152;
    17→            --accent-color: #9D5EB0;
    18→            --accent-dark: #6A3877;
    19→        }
    20→
    21→        body {
    22→            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, sans-serif;
    23→            color: #333;
    24→            margin: 0;
    25→            padding: 0;
    26→        }
    27→
    28→        .hero {
    29→            background: linear-gradient(135deg, var(--secondary-dark) 0%, var(--secondary-color) 50%, var(--primary-dark) 100%);
    30→            color: white;
    31→            padding: 5rem 2rem;
    32→            text-align: center;
    33→            position: relative;
    34→        }
    35→
    36→        .logo {
    37→            max-width: 120px;
    38→            margin-bottom: 2rem;
    39→            filter: drop-shadow(0 4px 8px rgba(0,0,0,0.2));
    40→        }
    41→
    42→        h1 {
    43→            font-size: 3rem;
    44→            font-weight: 800;
    45→            margin-bottom: 1rem;
    46→            text-shadow: 2px 2px 4px rgba(0,0,0,0.3);
    47→        }
    48→
    49→        .lead {
    50→            font-size: 1.3rem;
    51→            margin-bottom: 2.5rem;
    52→            opacity: 0.95;
    53→        }
    54→
    55→        .stats {
    56→            display: flex;
    57→            justify-content: center;
    58→            gap: 3rem;
    59→            margin: 2.5rem 0;
    60→            flex-wrap: wrap;
    61→        }
    62→
    63→        .stat-item {
    64→            text-align: center;
    65→        }
    66→
    67→        .stat-number {
    68→            font-size: 2.5rem;
    69→            font-weight: 800;
    70→            color: var(--primary-light);
    71→        }
    72→
    73→        .stat-label {
    74→            font-size: 0.95rem;
    75→            opacity: 0.9;
    76→            margin-top: 0.25rem;
    77→        }
    78→
    79→        .buttons {
    80→            display: flex;
    81→            justify-content: center;
    82→            gap: 1rem;
    83→            flex-wrap: wrap;
    84→            margin-top: 2rem;
    85→        }
    86→
    87→        .button {
    88→            display: inline-block;
    89→            padding: 0.875rem 2rem;
    90→            border-radius: 8px;
    91→            font-weight: 600;
    92→            text-decoration: none;
    93→            transition: all 0.3s;
    94→            font-size: 1.05rem;
    95→        }
    96→
    97→        .button-primary {
    98→            background-color: var(--primary-color);
    99→            color: white;
   100→        }
   101→
   102→        .button-primary:hover {
   103→            background-color: var(--primary-dark);
   104→            transform: translateY(-2px);
   105→            box-shadow: 0 4px 12px rgba(16, 155, 129, 0.3);
   106→            color: white;
   107→        }
   108→
   109→        .button-secondary {
   110→            border: 2px solid white;
   111→            color: white;
   112→        }
   113→
   114→        .button-secondary:hover {
   115→            background-color: white;
   116→            color: var(--secondary-color);
   117→        }
   118→
   119→        .tools-section {
   120→            padding: 4rem 2rem;
   121→            max-width: 1200px;
   122→            margin: 0 auto;
   123→        }
   124→
   125→        .tools-section h2 {
   126→            text-align: center;
   127→            color: var(--secondary-color);
   128→            font-weight: 700;
   129→            margin-bottom: 3rem;
   130→            font-size: 2.25rem;
   131→        }
   132→
   133→        .tool-grid {
   134→            display: grid;
   135→            grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
   136→            gap: 2rem;
   137→            margin-bottom: 3rem;
   138→        }
   139→
   140→        .tool-card {
   141→            background: white;
   142→            border-radius: 12px;
   143→            padding: 2rem;
   144→            box-shadow: 0 4px 6px rgba(0,0,0,0.05);
   145→            transition: all 0.3s;
   146→            text-decoration: none;
   147→            color: inherit;
   148→            display: block;
   149→        }
   150→
   151→        .tool-card:hover {
   152→            box-shadow: 0 8px 15px rgba(0,0,0,0.1);
   153→            transform: translateY(-5px);
   154→            text-decoration: none;
   155→            color: inherit;
   156→        }
   157→
   158→        .tool-icon {
   159→            font-size: 2.5rem;
   160→            color: var(--primary-color);
   161→            margin-bottom: 1rem;
   162→        }
   163→
   164→        .tool-card h3 {
   165→            color: var(--secondary-color);
   166→            font-weight: 700;
   167→            margin-bottom: 0.75rem;
   168→            font-size: 1.35rem;
   169→        }
   170→
   171→        .tool-card p {
   172→            color: #666;
   173→            line-height: 1.6;
   174→            margin-bottom: 1rem;
   175→        }
   176→
   177→        .tool-card ul {
   178→            list-style: none;
   179→            padding: 0;
   180→            margin: 0;
   181→        }
   182→
   183→        .tool-card li {
   184→            padding: 0.4rem 0;
   185→            color: #666;
   186→            font-size: 0.9rem;
   187→        }
   188→
   189→        .tool-card li i {
   190→            color: var(--primary-color);
   191→            margin-right: 0.5rem;
   192→        }
   193→
   194→        .resources-section {
   195→            background: #f8f9fa;
   196→            padding: 3rem 2rem;
   197→        }
   198→
   199→        .resources-grid {
   200→            max-width: 1000px;
   201→            margin: 0 auto;
   202→            display: grid;
   203→            grid-template-columns: repeat(auto-fit, minmax(220px, 1fr));
   204→            gap: 1.5rem;
   205→        }
   206→
   207→        .resource-link {
   208→            background: white;
   209→            padding: 1.5rem;
   210→            border-radius: 10px;
   211→            text-decoration: none;
   212→            color: var(--secondary-color);
   213→            display: flex;
   214→            align-items: center;
   215→            gap: 1rem;
   216→            transition: all 0.3s;
   217→            box-shadow: 0 2px 4px rgba(0,0,0,0.05);
   218→        }
   219→
   220→        .resource-link:hover {
   221→            transform: translateX(5px);
   222→            box-shadow: 0 4px 8px rgba(0,0,0,0.1);
   223→            color: var(--primary-color);
   224→        }
   225→
   226→        .resource-icon {
   227→            font-size: 1.75rem;
   228→            color: var(--accent-color);
   229→        }
   230→
   231→        .resource-text {
   232→            flex: 1;
   233→        }
   234→
   235→        .resource-link h4 {
   236→            margin: 0;
   237→            font-size: 1.05rem;
   238→            font-weight: 600;
   239→        }
   240→
   241→        .resource-link p {
   242→            margin: 0.25rem 0 0 0;
   243→            font-size: 0.85rem;
   244→            color: #666;
   245→        }
   246→
   247→        .footer {
   248→            background-color: var(--secondary-dark);
   249→            color: rgba(255,255,255,0.8);
   250→            padding: 2rem;
   251→            text-align: center;
   252→        }
   253→
   254→        .footer a {
   255→            color: var(--primary-light);
   256→            text-decoration: none;
   257→        }
   258→
   259→        .footer a:hover {
   260→            color: white;
   261→        }
   262→
   263→        @media (max-width: 768px) {
   264→            h1 {
   265→                font-size: 2.25rem;
   266→            }
   267→            .lead {
   268→                font-size: 1.1rem;
   269→            }
   270→            .stat-number {
   271→                font-size: 2rem;
   272→            }
   273→            .stats {
   274→                gap: 1.5rem;
   275→            }
   276→        }
   277→    </style>
   278→</head>
   279→<body>
   280→    <!-- Hero Section -->
   281→    <section class="hero">
   282→        <img src="awesome-virome-hex.png" alt="Awesome-Virome Logo" class="logo">
   283→        <h1>Awesome-Virome</h1>
   284→        <p class="lead">A comprehensive, curated database of software tools for virome analysis</p>
   285→
   286→        <div class="stats">
   287→            <div class="stat-item">
   288→                <div class="stat-number">300+</div>
   289→                <div class="stat-label">Curated Tools</div>
   290→            </div>
   291→            <div class="stat-item">
   292→                <div class="stat-number">8</div>
   293→                <div class="stat-label">Major Categories</div>
   294→            </div>
   295→            <div class="stat-item">
   296→                <div class="stat-number">164</div>
   297→                <div class="stat-label">Active Repositories</div>
   298→            </div>
   299→        </div>
   300→
   301→        <div class="buttons">
   302→            <a href="dashboard.html" class="button button-primary">
   303→                <i class="bi bi-bar-chart-fill"></i> Interactive Dashboard
   304→            </a>
   305→            <a href="https://github.com/shandley/awesome-virome/blob/main/README.md" class="button button-secondary">
   306→                <i class="bi bi-book"></i> Browse Tools
   307→            </a>
   308→        </div>
   309→    </section>
   310→
   311→    <!-- Interactive Tools Section -->
   312→    <section class="tools-section">
   313→        <h2>Explore Interactively</h2>
   314→        <div class="tool-grid">
   315→            <a href="dashboard.html" class="tool-card">
   316→                <div class="tool-icon">
   317→                    <i class="bi bi-graph-up-arrow"></i>
   318→                </div>
   319→                <h3>Interactive Dashboard</h3>
   320→                <p>Visualize the entire virome analysis ecosystem at a glance</p>
   321→                <ul>
   322→                    <li><i class="bi bi-check-circle-fill"></i> Tool categorization treemap</li>
   323→                    <li><i class="bi bi-check-circle-fill"></i> Interactive network graph</li>
   324→                    <li><i class="bi bi-check-circle-fill"></i> Timeline visualization</li>
   325→                    <li><i class="bi bi-check-circle-fill"></i> Technology trends</li>
   326→                </ul>
   327→            </a>
   328→
   329→            <a href="comparison.html" class="tool-card">
   330→                <div class="tool-icon">
   331→                    <i class="bi bi-columns-gap"></i>
   332→                </div>
   333→                <h3>Tool Comparison</h3>
   334→                <p>Compare tools side-by-side to find the perfect fit</p>
   335→                <ul>
   336→                    <li><i class="bi bi-check-circle-fill"></i> Multi-tool comparison</li>
   337→                    <li><i class="bi bi-check-circle-fill"></i> Advanced filtering</li>
   338→                    <li><i class="bi bi-check-circle-fill"></i> Smart sorting</li>
   339→                    <li><i class="bi bi-check-circle-fill"></i> Export to CSV/JSON</li>
   340→                </ul>
   341→            </a>
   342→
   343→            <a href="selection-guide.html" class="tool-card">
   344→                <div class="tool-icon">
   345→                    <i class="bi bi-compass"></i>
   346→                </div>
   347→                <h3>Selection Guide</h3>
   348→                <p>Get personalized recommendations through our decision tree</p>
   349→                <ul>
   350→                    <li><i class="bi bi-check-circle-fill"></i> Simple questionnaire</li>
   351→                    <li><i class="bi bi-check-circle-fill"></i> Guided pathways</li>
   352→                    <li><i class="bi bi-check-circle-fill"></i> Tailored recommendations</li>
   353→                    <li><i class="bi bi-check-circle-fill"></i> Feature explanations</li>
   354→                </ul>
   355→            </a>
   356→        </div>
   357→    </section>
   358→
   359→    <!-- Resources Section -->
   360→    <section class="resources-section">
   361→        <div class="tools-section">
   362→            <h2>Additional Resources</h2>
   363→            <div class="resources-grid">
   364→                <a href="https://github.com/shandley/awesome-virome/blob/main/README.md" class="resource-link">
   365→                    <div class="resource-icon">
   366→                        <i class="bi bi-book"></i>
   367→                    </div>
   368→                    <div class="resource-text">
   369→                        <h4>Complete Tool List</h4>
   370→                        <p>Browse all 300+ tools</p>
   371→                    </div>
   372→                </a>
   373→
   374→                <a href="https://github.com/shandley/awesome-virome/blob/main/API.md" class="resource-link">
   375→                    <div class="resource-icon">
   376→                        <i class="bi bi-code-square"></i>
   377→                    </div>
   378→                    <div class="resource-text">
   379→                        <h4>API Documentation</h4>
   380→                        <p>Programmatic access</p>
   381→                    </div>
   382→                </a>
   383→
   384→                <a href="https://github.com/shandley/awesome-virome/blob/main/CONTRIBUTING.md" class="resource-link">
   385→                    <div class="resource-icon">
   386→                        <i class="bi bi-people"></i>
   387→                    </div>
   388→                    <div class="resource-text">
   389→                        <h4>Contributing Guide</h4>
   390→                        <p>Add or update tools</p>
   391→                    </div>
   392→                </a>
   393→
   394→                <a href="https://github.com/shandley/awesome-virome" class="resource-link" target="_blank">
   395→                    <div class="resource-icon">
   396→                        <i class="bi bi-github"></i>
   397→                    </div>
   398→                    <div class="resource-text">
   399→                        <h4>GitHub Repository</h4>
   400→                        <p>View source code</p>
   401→                    </div>
   402→                </a>
   403→            </div>
   404→        </div>
   405→    </section>
   406→
   407→    <!-- Footer -->
   408→    <footer class="footer">
   409→        <p>
   410→            <strong>Awesome-Virome</strong> - A curated database of viral analysis tools<br>
   411→            Maintained by <a href="https://github.com/shandley">Scott Handley</a> and contributors |
   412→            Licensed under <a href="https://github.com/shandley/awesome-virome/blob/main/LICENSE">MIT</a>
   413→        </p>
   414→    </footer>
   415→
   416→    <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/js/bootstrap.bundle.min.js"></script>
   417→</body>
   418→</html>
   419→

1 file changed, 380 insertions(+), 36 deletions(-)

To https://github.com/shandley/awesome-virome.git
   f8da16475..61fb79dbc  main -> main

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/landing-page.html has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
     1→<!DOCTYPE html>
     2→<html lang="en">
     3→<head>
     4→    <meta charset="UTF-8">
     5→    <meta name="viewport" content="width=device-width, initial-scale=1.0">
     6→    <title>Awesome-Virome - Curated Viral Analysis Tools</title>
     7→    <meta name="description" content="A comprehensive, curated database of 300+ software tools for virome analysis">
     8→    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.11.1/font/bootstrap-icons.css">
     9→    <style>
    10→        :root {
    11→            /* Shadcn-inspired color palette */
    12→            --background: 0 0% 100%;
    13→            --foreground: 222.2 84% 4.9%;
    14→            --card: 0 0% 100%;
    15→            --card-foreground: 222.2 84% 4.9%;
    16→            --popover: 0 0% 100%;
    17→            --popover-foreground: 222.2 84% 4.9%;
    18→            --primary: 162 73% 33%;
    19→            --primary-foreground: 210 40% 98%;
    20→            --secondary: 210 40% 96.1%;
    21→            --secondary-foreground: 222.2 47.4% 11.2%;
    22→            --muted: 210 40% 96.1%;
    23→            --muted-foreground: 215.4 16.3% 46.9%;
    24→            --accent: 210 40% 96.1%;
    25→            --accent-foreground: 222.2 47.4% 11.2%;
    26→            --border: 214.3 31.8% 91.4%;
    27→            --input: 214.3 31.8% 91.4%;
    28→            --ring: 162 73% 33%;
    29→
    30→            /* Project colors */
    31→            --virome-primary: #109b81;
    32→            --virome-dark: #0d7a66;
    33→            --virome-light: #e6f7f4;
    34→        }
    35→
    36→        * {
    37→            margin: 0;
    38→            padding: 0;
    39→            box-sizing: border-box;
    40→        }
    41→
    42→        body {
    43→            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
    44→            color: hsl(var(--foreground));
    45→            background-color: hsl(var(--background));
    46→            line-height: 1.6;
    47→        }
    48→
    49→        /* Navigation */
    50→        .nav {
    51→            background-color: hsl(var(--card));
    52→            border-bottom: 1px solid hsl(var(--border));
    53→            padding: 1rem 0;
    54→            position: sticky;
    55→            top: 0;
    56→            z-index: 50;
    57→            backdrop-filter: blur(8px);
    58→            background-color: rgba(255, 255, 255, 0.8);
    59→        }
    60→
    61→        .nav-container {
    62→            max-width: 1280px;
    63→            margin: 0 auto;
    64→            padding: 0 2rem;
    65→            display: flex;
    66→            justify-content: space-between;
    67→            align-items: center;
    68→        }
    69→
    70→        .nav-brand {
    71→            font-size: 1.25rem;
    72→            font-weight: 700;
    73→            color: hsl(var(--foreground));
    74→            text-decoration: none;
    75→        }
    76→
    77→        .nav-brand span {
    78→            color: var(--virome-primary);
    79→        }
    80→
    81→        .nav-links {
    82→            display: flex;
    83→            gap: 2rem;
    84→            align-items: center;
    85→            list-style: none;
    86→        }
    87→
    88→        .nav-link {
    89→            color: hsl(var(--muted-foreground));
    90→            text-decoration: none;
    91→            font-size: 0.875rem;
    92→            font-weight: 500;
    93→            transition: color 0.2s;
    94→        }
    95→
    96→        .nav-link:hover {
    97→            color: hsl(var(--foreground));
    98→        }
    99→
   100→        /* Hero Section */
   101→        .hero {
   102→            background-color: hsl(var(--background));
   103→            padding: 6rem 2rem 4rem;
   104→            text-align: center;
   105→        }
   106→
   107→        .hero-container {
   108→            max-width: 1100px;
   109→            margin: 0 auto;
   110→        }
   111→
   112→        .logo {
   113→            width: 100px;
   114→            height: 100px;
   115→            margin: 0 auto 2rem;
   116→            display: block;
   117→        }
   118→
   119→        .hero h1 {
   120→            font-size: 3.5rem;
   121→            font-weight: 900;
   122→            letter-spacing: -0.02em;
   123→            margin-bottom: 1rem;
   124→            color: hsl(var(--foreground));
   125→        }
   126→
   127→        .hero-description {
   128→            font-size: 1.25rem;
   129→            color: hsl(var(--muted-foreground));
   130→            margin-bottom: 3rem;
   131→            max-width: 700px;
   132→            margin-left: auto;
   133→            margin-right: auto;
   134→        }
   135→
   136→        /* Stats */
   137→        .stats {
   138→            display: grid;
   139→            grid-template-columns: repeat(3, 1fr);
   140→            gap: 2rem;
   141→            margin: 3rem auto 3rem;
   142→            max-width: 800px;
   143→        }
   144→
   145→        .stat-card {
   146→            background: hsl(var(--card));
   147→            border: 1px solid hsl(var(--border));
   148→            border-radius: 0.75rem;
   149→            padding: 2rem 1.5rem;
   150→            text-align: center;
   151→            transition: all 0.2s;
   152→        }
   153→
   154→        .stat-card:hover {
   155→            border-color: var(--virome-primary);
   156→            box-shadow: 0 4px 12px rgba(16, 155, 129, 0.1);
   157→        }
   158→
   159→        .stat-number {
   160→            font-size: 2.5rem;
   161→            font-weight: 700;
   162→            color: var(--virome-primary);
   163→            line-height: 1;
   164→        }
   165→
   166→        .stat-label {
   167→            margin-top: 0.5rem;
   168→            font-size: 0.875rem;
   169→            color: hsl(var(--muted-foreground));
   170→            font-weight: 500;
   171→        }
   172→
   173→        /* Buttons */
   174→        .button-group {
   175→            display: flex;
   176→            gap: 1rem;
   177→            justify-content: center;
   178→            flex-wrap: wrap;
   179→        }
   180→
   181→        .button {
   182→            display: inline-flex;
   183→            align-items: center;
   184→            gap: 0.5rem;
   185→            padding: 0.625rem 1.5rem;
   186→            border-radius: 0.5rem;
   187→            font-size: 0.875rem;
   188→            font-weight: 600;
   189→            text-decoration: none;
   190→            transition: all 0.2s;
   191→            border: 1px solid transparent;
   192→        }
   193→
   194→        .button-primary {
   195→            background-color: var(--virome-primary);
   196→            color: white;
   197→        }
   198→
   199→        .button-primary:hover {
   200→            background-color: var(--virome-dark);
   201→            box-shadow: 0 4px 12px rgba(16, 155, 129, 0.2);
   202→        }
   203→
   204→        .button-secondary {
   205→            background-color: hsl(var(--background));
   206→            color: hsl(var(--foreground));
   207→            border-color: hsl(var(--border));
   208→        }
   209→
   210→        .button-secondary:hover {
   211→            background-color: hsl(var(--accent));
   212→            border-color: hsl(var(--muted-foreground));
   213→        }
   214→
   215→        /* Sections */
   216→        .section {
   217→            padding: 5rem 2rem;
   218→        }
   219→
   220→        .section-muted {
   221→            background-color: hsl(var(--muted));
   222→        }
   223→
   224→        .section-container {
   225→            max-width: 1200px;
   226→            margin: 0 auto;
   227→        }
   228→
   229→        .section-header {
   230→            text-align: center;
   231→            margin-bottom: 3.5rem;
   232→        }
   233→
   234→        .section-title {
   235→            font-size: 2.25rem;
   236→            font-weight: 700;
   237→            letter-spacing: -0.02em;
   238→            margin-bottom: 0.75rem;
   239→            color: hsl(var(--foreground));
   240→        }
   241→
   242→        .section-subtitle {
   243→            font-size: 1.125rem;
   244→            color: hsl(var(--muted-foreground));
   245→        }
   246→
   247→        /* Tool Cards */
   248→        .tool-grid {
   249→            display: grid;
   250→            grid-template-columns: repeat(auto-fit, minmax(320px, 1fr));
   251→            gap: 2rem;
   252→        }
   253→
   254→        .tool-card {
   255→            background: hsl(var(--card));
   256→            border: 1px solid hsl(var(--border));
   257→            border-radius: 0.75rem;
   258→            padding: 2rem;
   259→            text-decoration: none;
   260→            color: inherit;
   261→            display: block;
   262→            transition: all 0.2s;
   263→        }
   264→
   265→        .tool-card:hover {
   266→            border-color: var(--virome-primary);
   267→            box-shadow: 0 8px 24px rgba(0, 0, 0, 0.06);
   268→            transform: translateY(-2px);
   269→        }
   270→
   271→        .tool-icon {
   272→            width: 3rem;
   273→            height: 3rem;
   274→            background-color: var(--virome-light);
   275→            border-radius: 0.5rem;
   276→            display: flex;
   277→            align-items: center;
   278→            justify-content: center;
   279→            margin-bottom: 1.25rem;
   280→        }
   281→
   282→        .tool-icon i {
   283→            font-size: 1.5rem;
   284→            color: var(--virome-primary);
   285→        }
   286→
   287→        .tool-card h3 {
   288→            font-size: 1.25rem;
   289→            font-weight: 600;
   290→            margin-bottom: 0.75rem;
   291→            color: hsl(var(--foreground));
   292→        }
   293→
   294→        .tool-card p {
   295→            color: hsl(var(--muted-foreground));
   296→            margin-bottom: 1.25rem;
   297→            font-size: 0.9375rem;
   298→        }
   299→
   300→        .tool-features {
   301→            list-style: none;
   302→            display: flex;
   303→            flex-direction: column;
   304→            gap: 0.5rem;
   305→        }
   306→
   307→        .tool-features li {
   308→            display: flex;
   309→            align-items: center;
   310→            gap: 0.5rem;
   311→            font-size: 0.875rem;
   312→            color: hsl(var(--muted-foreground));
   313→        }
   314→
   315→        .tool-features i {
   316→            color: var(--virome-primary);
   317→            font-size: 1rem;
   318→        }
   319→
   320→        /* Resource Cards */
   321→        .resource-grid {
   322→            display: grid;
   323→            grid-template-columns: repeat(auto-fit, minmax(260px, 1fr));
   324→            gap: 1.5rem;
   325→        }
   326→
   327→        .resource-card {
   328→            background: hsl(var(--card));
   329→            border: 1px solid hsl(var(--border));
   330→            border-radius: 0.75rem;
   331→            padding: 1.5rem;
   332→            text-decoration: none;
   333→            color: inherit;
   334→            display: flex;
   335→            align-items: center;
   336→            gap: 1rem;
   337→            transition: all 0.2s;
   338→        }
   339→
   340→        .resource-card:hover {
   341→            border-color: var(--virome-primary);
   342→            background-color: var(--virome-light);
   343→        }
   344→
   345→        .resource-icon {
   346→            width: 2.5rem;
   347→            height: 2.5rem;
   348→            background-color: var(--virome-light);
   349→            border-radius: 0.5rem;
   350→            display: flex;
   351→            align-items: center;
   352→            justify-content: center;
   353→            flex-shrink: 0;
   354→        }
   355→
   356→        .resource-icon i {
   357→            font-size: 1.25rem;
   358→            color: var(--virome-primary);
   359→        }
   360→
   361→        .resource-content h4 {
   362→            font-size: 0.9375rem;
   363→            font-weight: 600;
   364→            margin-bottom: 0.25rem;
   365→            color: hsl(var(--foreground));
   366→        }
   367→
   368→        .resource-content p {
   369→            font-size: 0.8125rem;
   370→            color: hsl(var(--muted-foreground));
   371→            margin: 0;
   372→        }
   373→
   374→        /* CTA Section */
   375→        .cta-section {
   376→            background: linear-gradient(to bottom, hsl(var(--background)), hsl(var(--muted)));
   377→            border-top: 1px solid hsl(var(--border));
   378→            border-bottom: 1px solid hsl(var(--border));
   379→        }
   380→
   381→        /* Footer */
   382→        .footer {
   383→            background-color: hsl(var(--card));
   384→            border-top: 1px solid hsl(var(--border));
   385→            padding: 2.5rem 2rem;
   386→            text-align: center;
   387→        }
   388→
   389→        .footer-content {
   390→            max-width: 800px;
   391→            margin: 0 auto;
   392→        }
   393→
   394→        .footer p {
   395→            color: hsl(var(--muted-foreground));
   396→            font-size: 0.875rem;
   397→            line-height: 1.8;
   398→        }
   399→
   400→        .footer a {
   401→            color: var(--virome-primary);
   402→            text-decoration: none;
   403→            font-weight: 500;
   404→        }
   405→
   406→        .footer a:hover {
   407→            text-decoration: underline;
   408→        }
   409→
   410→        /* Responsive */
   411→        @media (max-width: 768px) {
   412→            .nav-links {
   413→                gap: 1rem;
   414→            }
   415→
   416→            .nav-link {
   417→                font-size: 0.8125rem;
   418→            }
   419→
   420→            .hero {
   421→                padding: 4rem 1.5rem 3rem;
   422→            }
   423→
   424→            .hero h1 {
   425→                font-size: 2.5rem;
   426→            }
   427→
   428→            .hero-description {
   429→                font-size: 1.125rem;
   430→            }
   431→
   432→            .stats {
   433→                grid-template-columns: 1fr;
   434→                gap: 1rem;
   435→            }
   436→
   437→            .stat-number {
   438→                font-size: 2rem;
   439→            }
   440→
   441→            .section {
   442→                padding: 3.5rem 1.5rem;
   443→            }
   444→
   445→            .section-title {
   446→                font-size: 1.875rem;
   447→            }
   448→
   449→            .tool-grid,
   450→            .resource-grid {
   451→                grid-template-columns: 1fr;
   452→            }
   453→        }
   454→    </style>
   455→</head>
   456→<body>
   457→    <!-- Navigation -->
   458→    <nav class="nav">
   459→        <div class="nav-container">
   460→            <a href="landing-page.html" class="nav-brand">Awesome-<span>Virome</span></a>
   461→            <ul class="nav-links">
   462→                <li><a href="dashboard.html" class="nav-link">Dashboard</a></li>
   463→                <li><a href="comparison.html" class="nav-link">Comparison</a></li>
   464→                <li><a href="selection-guide.html" class="nav-link">Selection Guide</a></li>
   465→                <li><a href="https://github.com/shandley/awesome-virome" class="nav-link"><i class="bi bi-github"></i> GitHub</a></li>
   466→            </ul>
   467→        </div>
   468→    </nav>
   469→
   470→    <!-- Hero Section -->
   471→    <section class="hero">
   472→        <div class="hero-container">
   473→            <img src="awesome-virome-hex.png" alt="Awesome-Virome" class="logo">
   474→            <h1>Awesome-Virome</h1>
   475→            <p class="hero-description">A comprehensive, curated database of software tools for virome analysis</p>
   476→
   477→            <div class="stats">
   478→                <div class="stat-card">
   479→                    <div class="stat-number">300+</div>
   480→                    <div class="stat-label">Curated Tools</div>
   481→                </div>
   482→                <div class="stat-card">
   483→                    <div class="stat-number">8</div>
   484→                    <div class="stat-label">Major Categories</div>
   485→                </div>
   486→                <div class="stat-card">
   487→                    <div class="stat-number">164</div>
   488→                    <div class="stat-label">Active Repositories</div>
   489→                </div>
   490→            </div>
   491→
   492→            <div class="button-group">
   493→                <a href="dashboard.html" class="button button-primary">
   494→                    <i class="bi bi-bar-chart-fill"></i>
   495→                    <span>Explore Dashboard</span>
   496→                </a>
   497→                <a href="https://github.com/shandley/awesome-virome/blob/main/README.md" class="button button-secondary">
   498→                    <i class="bi bi-book"></i>
   499→                    <span>Browse Tools</span>
   500→                </a>
   501→            </div>
   502→        </div>
   503→    </section>
   504→
   505→    <!-- Interactive Tools Section -->
   506→    <section class="section">
   507→        <div class="section-container">
   508→            <div class="section-header">
   509→                <h2 class="section-title">Explore Interactively</h2>
   510→                <p class="section-subtitle">Discover and compare viral analysis tools with our interactive web applications</p>
   511→            </div>
   512→
   513→            <div class="tool-grid">
   514→                <a href="dashboard.html" class="tool-card">
   515→                    <div class="tool-icon">
   516→                        <i class="bi bi-graph-up-arrow"></i>
   517→                    </div>
   518→                    <h3>Interactive Dashboard</h3>
   519→                    <p>Visualize the entire virome analysis ecosystem at a glance</p>
   520→                    <ul class="tool-features">
   521→                        <li><i class="bi bi-check-circle-fill"></i> Tool categorization treemap</li>
   522→                        <li><i class="bi bi-check-circle-fill"></i> Interactive network graph</li>
   523→                        <li><i class="bi bi-check-circle-fill"></i> Timeline visualization</li>
   524→                        <li><i class="bi bi-check-circle-fill"></i> Technology trends analysis</li>
   525→                    </ul>
   526→                </a>
   527→
   528→                <a href="comparison.html" class="tool-card">
   529→                    <div class="tool-icon">
   530→                        <i class="bi bi-columns-gap"></i>
   531→                    </div>
   532→                    <h3>Tool Comparison</h3>
   533→                    <p>Compare tools side-by-side to find the perfect fit</p>
   534→                    <ul class="tool-features">
   535→                        <li><i class="bi bi-check-circle-fill"></i> Multi-tool comparison</li>
   536→                        <li><i class="bi bi-check-circle-fill"></i> Advanced filtering options</li>
   537→                        <li><i class="bi bi-check-circle-fill"></i> Smart sorting capabilities</li>
   538→                        <li><i class="bi bi-check-circle-fill"></i> Export to CSV/JSON</li>
   539→                    </ul>
   540→                </a>
   541→
   542→                <a href="selection-guide.html" class="tool-card">
   543→                    <div class="tool-icon">
   544→                        <i class="bi bi-compass"></i>
   545→                    </div>
   546→                    <h3>Selection Guide</h3>
   547→                    <p>Get personalized recommendations through our decision tree</p>
   548→                    <ul class="tool-features">
   549→                        <li><i class="bi bi-check-circle-fill"></i> Simple questionnaire</li>
   550→                        <li><i class="bi bi-check-circle-fill"></i> Guided pathways</li>
   551→                        <li><i class="bi bi-check-circle-fill"></i> Tailored recommendations</li>
   552→                        <li><i class="bi bi-check-circle-fill"></i> Feature explanations</li>
   553→                    </ul>
   554→                </a>
   555→            </div>
   556→        </div>
   557→    </section>
   558→
   559→    <!-- Resources Section -->
   560→    <section class="section section-muted">
   561→        <div class="section-container">
   562→            <div class="section-header">
   563→                <h2 class="section-title">Additional Resources</h2>
   564→                <p class="section-subtitle">Everything you need to get started with virome analysis</p>
   565→            </div>
   566→
   567→            <div class="resource-grid">
   568→                <a href="https://github.com/shandley/awesome-virome/blob/main/README.md" class="resource-card">
   569→                    <div class="resource-icon">
   570→                        <i class="bi bi-book"></i>
   571→                    </div>
   572→                    <div class="resource-content">
   573→                        <h4>Complete Tool List</h4>
   574→                        <p>Browse all 300+ tools</p>
   575→                    </div>
   576→                </a>
   577→
   578→                <a href="https://github.com/shandley/awesome-virome/blob/main/API.md" class="resource-card">
   579→                    <div class="resource-icon">
   580→                        <i class="bi bi-code-square"></i>
   581→                    </div>
   582→                    <div class="resource-content">
   583→                        <h4>API Documentation</h4>
   584→                        <p>Programmatic access</p>
   585→                    </div>
   586→                </a>
   587→
   588→                <a href="https://github.com/shandley/awesome-virome/blob/main/CONTRIBUTING.md" class="resource-card">
   589→                    <div class="resource-icon">
   590→                        <i class="bi bi-people"></i>
   591→                    </div>
   592→                    <div class="resource-content">
   593→                        <h4>Contributing Guide</h4>
   594→                        <p>Add or update tools</p>
   595→                    </div>
   596→                </a>
   597→
   598→                <a href="https://github.com/shandley/awesome-virome" class="resource-card" target="_blank">
   599→                    <div class="resource-icon">
   600→                        <i class="bi bi-github"></i>
   601→                    </div>
   602→                    <div class="resource-content">
   603→                        <h4>GitHub Repository</h4>
   604→                        <p>View source code</p>
   605→                    </div>
   606→                </a>
   607→            </div>
   608→        </div>
   609→    </section>
   610→
   611→    <!-- CTA Section -->
   612→    <section class="section cta-section">
   613→        <div class="section-container">
   614→            <div class="section-header">
   615→                <h2 class="section-title">Ready to Start Your Virome Analysis?</h2>
   616→                <p class="section-subtitle">Explore 300+ tools, compare options, and find the perfect fit for your research</p>
   617→            </div>
   618→
   619→            <div class="button-group">
   620→                <a href="dashboard.html" class="button button-primary">
   621→                    <i class="bi bi-bar-chart-fill"></i>
   622→                    <span>Launch Dashboard</span>
   623→                </a>
   624→                <a href="https://github.com/shandley/awesome-virome" class="button button-secondary">
   625→                    <i class="bi bi-github"></i>
   626→                    <span>View on GitHub</span>
   627→                </a>
   628→            </div>
   629→        </div>
   630→    </section>
   631→
   632→    <!-- Footer -->
   633→    <footer class="footer">
   634→        <div class="footer-content">
   635→            <p>
   636→                <strong>Awesome-Virome</strong> - A curated database of viral analysis tools<br>
   637→                Maintained by <a href="https://github.com/shandley">Scott Handley</a> and contributors |
   638→                Licensed under <a href="https://github.com/shandley/awesome-virome/blob/main/LICENSE">MIT</a>
   639→            </p>
   640→        </div>
   641→    </footer>
   642→</body>
   643→</html>
   644→

1 file changed, 443 insertions(+), 218 deletions(-)

To https://github.com/shandley/awesome-virome.git
   61fb79dbc..7afc2ed89  main -> main

f8da16475 Phase 3 Complete: Create professional landing page
2b6947cb7 Set default version to 1.0.0 with mike 2.1.3
841903c07 Fix navigation links to use standard filenames
4dc18b4a5 Implement D3.js network graph and Chart.js analytics visualizations
c305d6780 D3 visualization push
64c2b9af0 added the ability to check crossref when semantic scholar can not find citations
e0de29307 fixed DOI formatting
f14b82e37 updated how citations are displayed
7f15b0a4d fixed perc. code covereage calculation
71bc178ca Merge branch 'main' into enhance_metadata
1f4e4fea4 Fix JavaScript errors and browser caching issues
2bb0bde26 minor fixes
1d8a65a4b complete dashboard overhaul
e6dc546b0 Merge pull request #8 from shandley/enhance_metadata
20f4839c2 added citation viz
4ff1e6676 minor updates
1a5dbb882 visual page improvements
cf14682ac fixes to the visualization
af178d937 first add of interactive viz site
198baef22 remove interactive viz

<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <meta http-equiv="Cache-Control" content="no-cache, no-store, must-revalidate">
    <meta http-equiv="Pragma" content="no-cache">
    <meta http-equiv="Expires" content="0">
    <title>Awesome-Virome Dashboard</title>
    <meta http-equiv="refresh" content="0;url=dashboard.html">
    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/css/bootstrap.min.css">
    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.11.1/font/bootstrap-icons.css">
    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/datatables.net-bs5@1.13.6/css/dataTables.bootstrap5.min.css">
    <style>
        :root {
            /* Modern virology-themed color palette */
            --primary-color: #109b81; /* Teal green */
            --primary-light: #6FC3BA;
            --primary-dark: #097362;
            --secondary-color: #2C4B7C; /* Deep blue */
            --secondary-light: #557EBF;
            --secondary-dark: #193152;
            --accent-color: #9D5EB0; /* Purple for viruses */
            --accent-light: #C89AD3;
            --accent-dark: #6A3877;
            --info-color: #3498db; /* Blue for info */
            --success-color: #28a745; /* Green for success */
            --warning-color: #ffc107; /* Yellow for warnings */
            --danger-color: #e74c3c; /* Red for errors */
            --light-bg: #f8f9fa;
            --dark-bg: #1E293B; /* Dark slate blue */
            --card-bg: #ffffff;
            --card-bg-dark: #334155;
            --card-shadow: 0 4px 6px rgba(0, 0, 0, 0.05);
            --card-shadow-hover: 0 8px 15px rgba(0, 0, 0, 0.1);
            --transition-speed: 0.3s;
            --border-radius: 12px;
            --section-padding: 2rem;
            --card-spacing: 1.5rem;
            --nav-height: 4rem;
            
            /* Category-specific colors */
            --color-identification: #4682B4; /* Steel Blue */
            --color-host: #6A5ACD; /* Slate Blue */
            --color-genome: #20B2AA; /* Light Sea Green */
            --color-taxonomy: #DB7093; /* Pale Violet Red */
            --color-functional: #9370DB; /* Medium Purple */
            --color-structural: #4169E1; /* Royal Blue */
            --color-crispr: #FF6347; /* Tomato */
            --color-database: #3CB371; /* Medium Sea Green */
            --color-sequence: #1E90FF; /* Dodger Blue */
            --color-visualization: #FF8C00; /* Dark Orange */
        }
        
        /* Dark mode variables */
        [data-theme="dark"] {
            --primary-color: #1AB394;
            --primary-light: #5BD6BC;
            --primary-dark: #0D8A70;
            --light-bg: #1E293B;
            --dark-bg: #0F172A;
            --card-bg: #334155;
            --card-bg-dark: #1E293B;
            --card-shadow: 0 4px 6px rgba(0, 0, 0, 0.2);
            --card-shadow-hover: 0 8px 15px rgba(0, 0, 0, 0.3);
            color: #E2E8F0;
        }
        
        body {
            font-family: 'Inter', 'Segoe UI', system-ui, -apple-system, sans-serif;
            background-color: var(--light-bg);
            color: #333;
            transition: background-color var(--transition-speed), color var(--transition-speed);
            line-height: 1.6;
            scroll-behavior: smooth;
        }
        
        [data-theme="dark"] body {
            color: #E2E8F0;
        }
        
        /* Dark mode toggle */
        .theme-toggle {
            background: none;
            border: none;
            cursor: pointer;
            width: 40px;
            height: 40px;
            border-radius: 50%;
            display: flex;
            align-items: center;
            justify-content: center;
            color: #fff;
            margin-left: 1rem;
            outline: none;
            position: relative;
            transition: all var(--transition-speed);
        }
        
        .theme-toggle:hover {

    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>Awesome-Virome - Curated Viral Analysis Tools</title>
    <meta name="description" content="A comprehensive, curated database of 300+ software tools for virome analysis">
    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/css/bootstrap.min.css">
    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.11.1/font/bootstrap-icons.css">
--
        <img src="awesome-virome-hex.png" alt="Awesome-Virome Logo" class="logo">
        <h1>Awesome-Virome</h1>
        <p class="lead">A comprehensive, curated database of software tools for virome analysis</p>

        <div class="stats">
--
                </div>
                <h3>Interactive Dashboard</h3>
                <p>Visualize the entire virome analysis ecosystem at a glance</p>
                <ul>
                    <li><i class="bi bi-check-circle-fill"></i> Tool categorization treemap</li>
--
                    </div>
                    <div class="resource-text">
                        <h4>API Documentation</h4>
                        <p>Programmatic access</p>
                    </div>

7afc2ed89 Redesign landing page with shadcn-inspired styling
61fb79dbc Enhance landing-page.html with comprehensive content
ad4381000 Fix GitHub Pages deployment to support both dashboard and MkDocs

<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>Awesome-Virome</title>
    <style>
        body {
            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Open Sans', 'Helvetica Neue', sans-serif;
            line-height: 1.6;
            color: #333;
            max-width: 800px;
            margin: 0 auto;
            padding: 2rem;
            text-align: center;
        }
        .logo {
            max-width: 150px;
            margin-bottom: 2rem;
        }
        h1 {
            color: #2C4B7C;
            margin-bottom: 1rem;
        }
        p {
            margin-bottom: 2rem;
            font-size: 1.1rem;
        }
        .buttons {
            display: flex;
            justify-content: center;
            gap: 1rem;
            flex-wrap: wrap;
        }
        .button {
            display: inline-block;
            background-color: #109b81;
            color: white;
            text-decoration: none;
            padding: 1rem 2rem;
            border-radius: 8px;
            font-weight: 600;
            transition: transform 0.2s, background-color 0.2s;
        }
        .button:hover {
            background-color: #097362;
            transform: translateY(-3px);
        }
        .button.secondary {
            background-color: #2C4B7C;
        }
        .button.secondary:hover {
            background-color: #193152;
        }
        .github-link {
            margin-top: 3rem;
            display: block;
            color: #666;
        }
    </style>
</head>
<body>
    <img src="awesome-virome-hex.png" alt="Awesome-Virome Logo" class="logo">
    <h1>Welcome to Awesome-Virome</h1>
    <p>A curated collection of virology bioinformatics tools and resources</p>
    
    <div class="buttons">
        <a href="dashboard.html" class="button">Interactive Dashboard</a>
        <a href="1.0.0/" class="button secondary">Documentation</a>
    </div>
    
    <a href="https://github.com/shandley/awesome-virome" class="github-link" target="_blank">View on GitHub</a>
</body>
</html>

./archive/deprecated_docs
./docs
./mkdocs
./mkdocs/mkdocs.yml
./mkdocs/docs
./mkdocs/site
./reports/site_health.md

total 32
drwxr-xr-x@  8 scotthandley  staff   256 Nov 29 15:06 .
drwxr-xr-x@ 49 scotthandley  staff  1568 Nov 29 16:11 ..
drwxr-xr-x@  9 scotthandley  staff   288 May  4  2025 docs
-rw-r--r--@  1 scotthandley  staff  4493 May  4  2025 MKDOCS_IMPLEMENTATION.md
-rw-r--r--@  1 scotthandley  staff  2978 May  4  2025 mkdocs.yml
drwxr-xr-x@  4 scotthandley  staff   128 May  4  2025 overrides
-rw-r--r--@  1 scotthandley  staff    48 May  4  2025 requirements.txt
drwxr-xr-x@ 13 scotthandley  staff   416 May  4  2025 site

total 8
drwxr-xr-x@ 9 scotthandley  staff   288 May  4  2025 .
drwxr-xr-x@ 8 scotthandley  staff   256 Nov 29 15:06 ..
drwxr-xr-x@ 5 scotthandley  staff   160 May  4  2025 api
drwxr-xr-x@ 7 scotthandley  staff   224 May  4  2025 assets
drwxr-xr-x@ 5 scotthandley  staff   160 May  4  2025 contributing
-rw-r--r--@ 1 scotthandley  staff  2102 May  4  2025 index.md
drwxr-xr-x@ 5 scotthandley  staff   160 May  4  2025 intro
drwxr-xr-x@ 4 scotthandley  staff   128 May  4  2025 js
drwxr-xr-x@ 6 scotthandley  staff   192 May  4  2025 tools

total 40
drwxr-xr-x@ 5 scotthandley  staff   160 May  4  2025 .
drwxr-xr-x@ 9 scotthandley  staff   288 May  4  2025 ..
-rw-r--r--@ 1 scotthandley  staff  3236 May  4  2025 index.md
-rw-r--r--@ 1 scotthandley  staff  2223 May  4  2025 versioning.md
-rw-r--r--@ 1 scotthandley  staff  8519 May  4  2025 workflows.md

     1→site_name: Awesome-Virome
     2→site_url: https://shandley.github.io/awesome-virome/
     3→repo_url: https://github.com/shandley/awesome-virome
     4→repo_name: shandley/awesome-virome
     5→edit_uri: edit/main/mkdocs/docs/
     6→
     7→theme:
     8→  name: material
     9→  logo: assets/awesome-virome-hex.png
    10→  favicon: assets/awesome-virome-hex.png
    11→  palette:
    12→    # Palette toggle for light mode
    13→    - media: "(prefers-color-scheme: light)"
    14→      scheme: default
    15→      primary: indigo
    16→      accent: indigo
    17→      toggle:
    18→        icon: material/brightness-7
    19→        name: Switch to dark mode
    20→    # Palette toggle for dark mode
    21→    - media: "(prefers-color-scheme: dark)"
    22→      scheme: slate
    23→      primary: indigo
    24→      accent: indigo
    25→      toggle:
    26→        icon: material/brightness-4
    27→        name: Switch to light mode
    28→  features:
    29→    - navigation.instant
    30→    - navigation.tracking
    31→    - navigation.tabs
    32→    - navigation.sections
    33→    - navigation.indexes
    34→    - navigation.top
    35→    - navigation.footer
    36→    - content.tabs.link
    37→    - content.code.copy
    38→    - content.code.annotate
    39→    - search.highlight
    40→    - search.share
    41→    - search.suggest
    42→  icon:
    43→    admonition:
    44→      tool: material/tools
    45→  font:
    46→    text: Roboto
    47→    code: Roboto Mono
    48→  custom_dir: overrides
    49→
    50→extra_css:
    51→  - assets/stylesheets/extra.css
    52→
    53→extra_javascript:
    54→  - https://cdn.jsdelivr.net/npm/mermaid@9.4.3/dist/mermaid.min.js
    55→  - js/mermaid.js
    56→
    57→# Extensions
    58→markdown_extensions:
    59→  - admonition
    60→  - pymdownx.details
    61→  - pymdownx.superfences:
    62→      custom_fences:
    63→        - name: mermaid
    64→          class: mermaid
    65→          format: !!python/name:pymdownx.superfences.fence_div_format
    66→  - pymdownx.highlight:
    67→      anchor_linenums: true
    68→      line_spans: __span
    69→      pygments_lang_class: true
    70→  - pymdownx.inlinehilite
    71→  - pymdownx.snippets
    72→  - pymdownx.tabbed:
    73→      alternate_style: true
    74→  - tables
    75→  - footnotes
    76→  - attr_list
    77→  - md_in_html
    78→
    79→# Plugins
    80→plugins:
    81→  - search
    82→  - mike:
    83→      version_selector: true
    84→      canonical_version: latest
    85→
    86→# Navigation structure
    87→nav:
    88→  - Home: index.md
    89→  - Getting Started:
    90→    - Introduction: intro/index.md
    91→    - Typical Workflows: intro/workflows.md
    92→    - Versioning: intro/versioning.md
    93→  - Core Analysis Tools:
    94→    - Overview: tools/overview.md
    95→    - Virus Identification: tools/virus-identification.md
    96→    - Host Prediction: tools/host-prediction.md
    97→    - Selection Guide: tools/selection-guide.md
    98→  - API Reference:
    99→    - Overview: api/overview.md
   100→    - Endpoints: api/endpoints.md
   101→    - Examples: api/examples.md
   102→  - Contributing:
   103→    - Guidelines: contributing/guidelines.md
   104→    - Validation: contributing/validation.md
   105→    - Updating Docs: contributing/updating-docs.md
   106→
   107→# Extra settings
   108→extra:
   109→  social:
   110→    - icon: fontawesome/brands/github
   111→      link: https://github.com/shandley/awesome-virome
   112→  homepage: home.html
   113→  version:
   114→    provider: mike
   115→    default: latest
   116→
   117→copyright: >
   118→  &copy; 2023-2025 <a href="https://github.com/shandley">Scott Handley</a> - 
   119→  <a href="#__consent">Change cookie settings</a>

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

     1→# Typical Virome Analysis Workflows
     2→
     3→This page outlines common workflows for virome analysis, showcasing how different tools from the Awesome-Virome collection can be combined to achieve specific research goals.
     4→
     5→<!-- Mermaid diagrams are initialized by the mermaid.js script included in mkdocs.yml -->
     6→
     7→## Basic Virome Analysis Workflow
     8→
     9→For general metagenomic virome analysis, this basic workflow provides a solid foundation:
    10→
    11→<div class="workflow-container">
    12→  <div class="workflow">
    13→    <div class="workflow-box">Raw Sequencing Data</div>
    14→    <div class="workflow-arrow">→</div>
    15→    <div class="workflow-box">Quality Control</div>
    16→    <div class="workflow-arrow">→</div>
    17→    <div class="workflow-box">Assembly</div>
    18→    <div class="workflow-arrow">→</div>
    19→    <div class="workflow-box">Viral Contig Identification</div>
    20→  </div>
    21→  <div class="workflow">
    22→    <div class="workflow-box">Functional Annotation</div>
    23→    <div class="workflow-arrow">←</div>
    24→    <div class="workflow-box">Host Prediction</div>
    25→    <div class="workflow-arrow">←</div>
    26→    <div class="workflow-box">Taxonomic Classification</div>
    27→    <div class="workflow-arrow">←</div>
    28→    <div class="workflow-box">Quality Assessment</div>
    29→  </div>
    30→</div>
    31→
    32→### Step-by-Step Guide
    33→
    34→<ol>
    35→<li><strong>Quality Control of Metagenomic Reads</strong><br>
    36→<ul>
    37→<li><strong>Tools:</strong> Standard bioinformatics QC tools (Trimmomatic, FastQC, etc.)</li>
    38→<li><strong>Purpose:</strong> Remove low-quality reads, adapters, and contaminants</li>
    39→</ul>
    40→</li>
    41→
    42→<li><strong>Assembly of Contigs</strong><br>
    43→<ul>
    44→<li><strong>Tools:</strong> SPAdes, MEGAHIT</li>
    45→<li><strong>Purpose:</strong> Assemble short reads into longer contiguous sequences (contigs)</li>
    46→</ul>
    47→</li>
    48→
    49→<li><strong>Identification of Viral Contigs</strong><br>
    50→<ul>
    51→<li><strong>Tools:</strong> VirSorter2, VIBRANT, geNomad</li>
    52→<li><strong>Purpose:</strong> Identify which contigs are of viral origin</li>
    53→</ul>
    54→</li>
    55→
    56→<li><strong>Quality Assessment</strong><br>
    57→<ul>
    58→<li><strong>Tools:</strong> CheckV</li>
    59→<li><strong>Purpose:</strong> Assess the completeness and quality of viral genomes</li>
    60→</ul>
    61→</li>
    62→
    63→<li><strong>Taxonomic Classification</strong><br>
    64→<ul>
    65→<li><strong>Tools:</strong> vConTACT2, PhaGCN</li>
    66→<li><strong>Purpose:</strong> Assign taxonomy to viral sequences</li>
    67→</ul>
    68→</li>
    69→
    70→<li><strong>Host Prediction</strong><br>
    71→<ul>
    72→<li><strong>Tools:</strong> iPHoP, CHERRY</li>
    73→<li><strong>Purpose:</strong> Predict the bacterial hosts of phages</li>
    74→</ul>
    75→</li>
    76→
    77→<li><strong>Functional Annotation</strong><br>
    78→<ul>
    79→<li><strong>Tools:</strong> Pharokka, DRAMv</li>
    80→<li><strong>Purpose:</strong> Annotate genes and predict functions</li>
    81→</ul>
    82→</li>
    83→</ol>
    84→
    85→## RNA Virus Discovery Workflow
    86→
    87→For specifically focusing on RNA viruses in your samples:
    88→
    89→<div class="workflow-container">
    90→  <div class="workflow">
    91→    <div class="workflow-box">Raw RNA-Seq Data</div>
    92→    <div class="workflow-arrow">→</div>
    93→    <div class="workflow-box">Quality Control</div>
    94→    <div class="workflow-arrow">→</div>
    95→    <div class="workflow-box">Assembly</div>
    96→    <div class="workflow-arrow">→</div>
    97→    <div class="workflow-box">RdRp Search</div>
    98→  </div>
    99→  <div class="workflow">
   100→    <div class="workflow-box">Phylogenetic Analysis</div>
   101→    <div class="workflow-arrow">←</div>
   102→    <div class="workflow-box">Genome Annotation</div>
   103→    <div class="workflow-arrow">←</div>
   104→    <div class="workflow-box">RNA Virus Verification</div>
   105→  </div>
   106→</div>
   107→
   108→### Key Tools for RNA Virus Analysis
   109→
   110→<ol>
   111→<li><strong>RNA Virus Detection</strong><br>
   112→<ul>
   113→<li><strong>Tools:</strong> palmID, RdRp-scan, metaviralSPAdes-RNA</li>
   114→<li><strong>Purpose:</strong> Identify RNA virus sequences by detecting conserved RdRp domains</li>
   115→</ul>
   116→</li>
   117→
   118→<li><strong>RNA Virus Annotation</strong><br>
   119→<ul>
   120→<li><strong>Tools:</strong> VirMine-RNA</li>
   121→<li><strong>Purpose:</strong> Functional annotation specific to RNA viral genomes</li>
   122→</ul>
   123→</li>
   124→</ol>
   125→
   126→## Prophage Identification Workflow
   127→
   128→For identifying integrated prophages in bacterial genomes:
   129→
   130→<div class="workflow-container">
   131→  <div class="workflow">
   132→    <div class="workflow-box">Bacterial Genome</div>
   133→    <div class="workflow-arrow">→</div>
   134→    <div class="workflow-box">Prophage Detection</div>
   135→    <div class="workflow-arrow">→</div>
   136→    <div class="workflow-box">Prophage Excision</div>
   137→  </div>
   138→  <div class="workflow">
   139→    <div class="workflow-box">Host-Prophage Interaction Analysis</div>
   140→    <div class="workflow-arrow">←</div>
   141→    <div class="workflow-box">Prophage Annotation</div>
   142→    <div class="workflow-arrow">←</div>
   143→    <div class="workflow-box">Prophage Verification</div>
   144→  </div>
   145→</div>
   146→
   147→### Key Tools for Prophage Analysis
   148→
   149→<ol>
   150→<li><strong>Prophage Detection</strong><br>
   151→<ul>
   152→<li><strong>Tools:</strong> PhiSpy, Phigaro, PHASTER</li>
   153→<li><strong>Purpose:</strong> Identify integrated viral sequences within bacterial genomes</li>
   154→</ul>
   155→</li>
   156→
   157→<li><strong>Prophage Analysis</strong><br>
   158→<ul>
   159→<li><strong>Tools:</strong> viralintegration, hafeZ</li>
   160→<li><strong>Purpose:</strong> Analyze integration sites and characterize prophage regions</li>
   161→</ul>
   162→</li>
   163→</ol>
   164→
   165→## Advanced Workflows
   166→
   167→These more specialized workflows address specific research questions:
   168→
   169→### Viral Quasispecies Analysis
   170→
   171→For analyzing viral population diversity within a sample:
   172→
   173→<ol>
   174→<li><strong>Strain Reconstruction</strong><br>
   175→<ul>
   176→<li><strong>Tools:</strong> VStrains, COBRA</li>
   177→<li><strong>Purpose:</strong> Reconstruct individual viral strains from complex metagenomic samples</li>
   178→</ul>
   179→</li>
   180→
   181→<li><strong>Quasispecies Analysis</strong><br>
   182→<ul>
   183→<li><strong>Tools:</strong> ShoRAH, CliqueSNV</li>
   184→<li><strong>Purpose:</strong> Analyze genetic variation and population dynamics within viral communities</li>
   185→</ul>
   186→</li>
   187→</ol>
   188→
   189→### Virome-Host Interaction Analysis
   190→
   191→For studying how viruses interact with their hosts:
   192→
   193→<ol>
   194→<li><strong>CRISPR Analysis</strong><br>
   195→<ul>
   196→<li><strong>Tools:</strong> SpacePHARER, CrisprOpenDB</li>
   197→<li><strong>Purpose:</strong> Identify CRISPR spacers and predict virus-host relationships</li>
   198→</ul>
   199→</li>
   200→
   201→<li><strong>Protein-Protein Interactions</strong><br>
   202→<ul>
   203→<li><strong>Tools:</strong> DeepVHPPI</li>
   204→<li><strong>Purpose:</strong> Predict interactions between viral and host proteins</li>
   205→</ul>
   206→</li>
   207→</ol>
   208→
   209→## Recommended Tools by Category
   210→
   211→For newcomers to virome analysis, here are some recommended starting points:
   212→
   213→<ol>
   214→<li><strong>Viral identification</strong><br>
   215→<ul>
   216→<li><strong>Tools:</strong> VirSorter2, VIBRANT, geNomad</li>
   217→<li><strong>Difficulty:</strong> Beginner to Intermediate</li>
   218→<li><strong>Computational requirements:</strong> Moderate</li>
   219→</ul>
   220→</li>
   221→
   222→<li><strong>Host prediction</strong><br>
   223→<ul>
   224→<li><strong>Tools:</strong> iPHoP, CHERRY</li>
   225→<li><strong>Difficulty:</strong> Intermediate</li>
   226→<li><strong>Computational requirements:</strong> Moderate to High</li>
   227→</ul>
   228→</li>
   229→
   230→<li><strong>Genome annotation</strong><br>
   231→<ul>
   232→<li><strong>Tools:</strong> Pharokka, DRAMv</li>
   233→<li><strong>Difficulty:</strong> Beginner</li>
   234→<li><strong>Computational requirements:</strong> Low to Moderate</li>
   235→</ul>
   236→</li>
   237→
   238→<li><strong>Taxonomy assignment</strong><br>
   239→<ul>
   240→<li><strong>Tools:</strong> vConTACT2, PhaGCN</li>
   241→<li><strong>Difficulty:</strong> Intermediate</li>
   242→<li><strong>Computational requirements:</strong> Moderate</li>
   243→</ul>
   244→</li>
   245→
   246→<li><strong>Quality control</strong><br>
   247→<ul>
   248→<li><strong>Tools:</strong> CheckV</li>
   249→<li><strong>Difficulty:</strong> Beginner</li>
   250→<li><strong>Computational requirements:</strong> Low</li>
   251→</ul>
   252→</li>
   253→</ol>
   254→
   255→## Next Steps
   256→
   257→<ol>
   258→<li><strong>Explore Tools</strong><br>
   259→<ul>
   260→<li>Visit the <a href="../../tools/overview/">Tools Overview</a> section for detailed information about each tool</li>
   261→<li>Check the <a href="../../tools/selection-guide/">Selection Guide</a> to find the best tools for your specific needs</li>
   262→</ul>
   263→</li>
   264→
   265→<li><strong>Learn About Data Access</strong><br>
   266→<ul>
   267→<li>Review the <a href="../../api/overview/">API Reference</a> to learn how to access the Awesome-Virome database programmatically</li>
   268→<li>See <a href="../../api/examples/">API Examples</a> for code snippets in Python, R, and JavaScript</li>
   269→</ul>
   270→</li>
   271→
   272→<li><strong>Join the Community</strong><br>
   273→<ul>
   274→<li>Contribute to the project by following our <a href="../../contributing/guidelines/">Contribution Guidelines</a></li>
   275→<li>Explore the <a href="https://github.com/shandley/awesome-virome">GitHub repository</a> for the latest updates</li>
   276→</ul>
   277→</li>
   278→</ol>

<system-reminder>
Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
</system-reminder>

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/landing-page.html has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
   488→                    <div class="stat-label">Active Repositories</div>
   489→                </div>
   490→            </div>
   491→
   492→            <div class="button-group">
   493→                <a href="dashboard.html" class="button button-primary">
   494→                    <i class="bi bi-bar-chart-fill"></i>
   495→                    <span>Explore Dashboard</span>
   496→                </a>
   497→                <a href="1.0.0/" class="button button-secondary">
   498→                    <i class="bi bi-book"></i>
   499→                    <span>Documentation</span>
   500→                </a>
   501→                <a href="https://github.com/shandley/awesome-virome/blob/main/README.md" class="button button-secondary">
   502→                    <i class="bi bi-list-ul"></i>
   503→                    <span>Browse Tools</span>
   504→                </a>
   505→            </div>
   506→        </div>
   507→    </section>
   508→
   509→    <!-- Interactive Tools Section -->

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/landing-page.html has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
   619→                <h2 class="section-title">Ready to Start Your Virome Analysis?</h2>
   620→                <p class="section-subtitle">Explore 300+ tools, compare options, and find the perfect fit for your research</p>
   621→            </div>
   622→
   623→            <div class="button-group">
   624→                <a href="dashboard.html" class="button button-primary">
   625→                    <i class="bi bi-bar-chart-fill"></i>
   626→                    <span>Launch Dashboard</span>
   627→                </a>
   628→                <a href="1.0.0/" class="button button-secondary">
   629→                    <i class="bi bi-book"></i>
   630→                    <span>Read Documentation</span>
   631→                </a>
   632→                <a href="https://github.com/shandley/awesome-virome" class="button button-secondary">
   633→                    <i class="bi bi-github"></i>
   634→                    <span>View on GitHub</span>
   635→                </a>
   636→            </div>
   637→        </div>
   638→    </section>
   639→
   640→    <!-- Footer -->

The file /Users/scotthandley/Code/awesome-virome/awesome-virome/landing-page.html has been updated. Here's the result of running `cat -n` on a snippet of the edited file:
   567→                <h2 class="section-title">Additional Resources</h2>
   568→                <p class="section-subtitle">Everything you need to get started with virome analysis</p>
   569→            </div>
   570→
   571→            <div class="resource-grid">
   572→                <a href="1.0.0/" class="resource-card">
   573→                    <div class="resource-icon">
   574→                        <i class="bi bi-book-half"></i>
   575→                    </div>
   576→                    <div class="resource-content">
   577→                        <h4>Workflow Documentation</h4>
   578→                        <p>Learn virome analysis</p>
   579→                    </div>
   580→                </a>
   581→
   582→                <a href="https://github.com/shandley/awesome-virome/blob/main/README.md" class="resource-card">
   583→                    <div class="resource-icon">
   584→                        <i class="bi bi-list-ul"></i>
   585→                    </div>
   586→                    <div class="resource-content">
   587→                        <h4>Complete Tool List</h4>
   588→                        <p>Browse all 300+ tools</p>
   589→                    </div>
   590→                </a>
   591→
   592→                <a href="https://github.com/shandley/awesome-virome/blob/main/API.md" class="resource-card">
   593→                    <div class="resource-icon">
   594→                        <i class="bi bi-code-square"></i>
   595→                    </div>
   596→                    <div class="resource-content">

1 file changed, 20 insertions(+), 2 deletions(-)

To https://github.com/shandley/awesome-virome.git
   7afc2ed89..2c2e9af0b  main -> main